From bc9aee94c0aa5987d0baa90adb4b733133110bb3 Mon Sep 17 00:00:00 2001 From: smarco Date: Mon, 25 Jul 2022 15:50:58 +0200 Subject: [PATCH] Factor wavefronts -> wavefront --- tests/wfa.utest.log | 896 +++++++++++++++---------------- wavefront/wavefront_aligner.c | 10 +- wavefront/wavefront_aligner.h | 2 +- wavefront/wavefront_backtrace.c | 72 +-- wavefront/wavefront_components.c | 12 +- wavefront/wavefront_components.h | 4 +- wavefront/wavefront_compute.c | 2 +- wavefront/wavefront_debug.c | 4 +- wavefront/wavefront_heuristic.c | 2 +- wavefront/wavefront_penalties.c | 138 ++--- wavefront/wavefront_penalties.h | 46 +- wavefront/wavefront_plot.c | 2 +- 12 files changed, 595 insertions(+), 595 deletions(-) diff --git a/tests/wfa.utest.log b/tests/wfa.utest.log index 6a4b909..7e93028 100644 --- a/tests/wfa.utest.log +++ b/tests/wfa.utest.log @@ -1,7 +1,7 @@ [Benchmark] => Total.reads 305 -=> Time.Benchmark 139.60 ms ( 1 call, 139.60 ms/call {min139.60ms,Max139.60ms}) - => Time.Alignment 122.64 ms ( 87.85 %) ( 305 calls, 402.11 us/call {min736ns,Max18.97ms}) +=> Time.Benchmark 123.50 ms ( 1 call, 123.50 ms/call {min123.50ms,Max123.50ms}) + => Time.Alignment 113.77 ms ( 92.12 %) ( 305 calls, 373.02 us/call {min227ns,Max17.75ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -13,20 +13,20 @@ => CIGAR.Insertions 19.08 Kbases ( 10.82 %) (samples=19K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 17.16 Kbases ( 9.73 %) (samples=17K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.indel.alg -a indel-wfa --check=correct" - User time (seconds): 0.12 + User time (seconds): 0.11 System time (seconds): 0.01 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.14 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.12 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 27360 + Maximum resident set size (kbytes): 27284 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 6276 + Minor (reclaiming a frame) page faults: 6274 Voluntary context switches: 1 - Involuntary context switches: 1 + Involuntary context switches: 0 Swaps: 0 File system inputs: 0 File system outputs: 256 @@ -37,8 +37,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 98.70 ms ( 1 call, 98.70 ms/call {min98.70ms,Max98.70ms}) - => Time.Alignment 90.47 ms ( 91.66 %) ( 305 calls, 296.62 us/call {min210ns,Max10.68ms}) +=> Time.Benchmark 116.99 ms ( 1 call, 116.99 ms/call {min116.99ms,Max116.99ms}) + => Time.Alignment 108.41 ms ( 92.67 %) ( 305 calls, 355.44 us/call {min222ns,Max17.49ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -50,18 +50,18 @@ => CIGAR.Insertions 10.30 Kbases ( 5.84 %) (samples=10K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 8.38 Kbases ( 4.75 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.edit.alg -a edit-wfa --check=correct" - User time (seconds): 0.08 + User time (seconds): 0.09 System time (seconds): 0.01 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.10 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 27036 + Maximum resident set size (kbytes): 26952 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 6269 + Minor (reclaiming a frame) page faults: 6267 Voluntary context switches: 1 Involuntary context switches: 1 Swaps: 0 @@ -74,8 +74,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.10 s ( 1 call, 1.10 s/call {min1.10s,Max1.10s}) - => Time.Alignment 1.09 s ( 99.19 %) ( 305 calls, 3.58 ms/call {min230ns,Max171.74ms}) +=> Time.Benchmark 1.04 s ( 1 call, 1.04 s/call {min1.04s,Max1.04s}) + => Time.Alignment 1.03 s ( 99.20 %) ( 305 calls, 3.39 ms/call {min227ns,Max165.06ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -87,20 +87,20 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.alg -a gap-affine-wfa --check=correct" - User time (seconds): 1.03 - System time (seconds): 0.07 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.11 + User time (seconds): 0.95 + System time (seconds): 0.09 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.05 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 281496 + Maximum resident set size (kbytes): 281428 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 69853 - Voluntary context switches: 1 - Involuntary context switches: 2 + Minor (reclaiming a frame) page faults: 69851 + Voluntary context switches: 2 + Involuntary context switches: 9 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -111,8 +111,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 5.58 s ( 1 call, 5.58 s/call {min5.58s,Max5.58s}) - => Time.Alignment 5.57 s ( 99.84 %) ( 305 calls, 18.25 ms/call {min230ns,Max1.00s}) +=> Time.Benchmark 5.67 s ( 1 call, 5.67 s/call {min5.67s,Max5.67s}) + => Time.Alignment 5.66 s ( 99.84 %) ( 305 calls, 18.55 ms/call {min223ns,Max1.04s}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -124,20 +124,20 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine2p.alg -a gap-affine2p-wfa --check=correct" - User time (seconds): 5.07 - System time (seconds): 0.56 + User time (seconds): 5.10 + System time (seconds): 0.61 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.63 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.72 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 1783236 + Maximum resident set size (kbytes): 1783240 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 445277 - Voluntary context switches: 2 - Involuntary context switches: 21 + Minor (reclaiming a frame) page faults: 445276 + Voluntary context switches: 1 + Involuntary context switches: 30 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -148,8 +148,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 473.31 ms ( 1 call, 473.31 ms/call {min473.31ms,Max473.31ms}) - => Time.Alignment 465.25 ms ( 98.30 %) ( 305 calls, 1.53 ms/call {min223ns,Max78.48ms}) +=> Time.Benchmark 557.05 ms ( 1 call, 557.05 ms/call {min557.05ms,Max557.05ms}) + => Time.Alignment 546.28 ms ( 98.07 %) ( 305 calls, 1.79 ms/call {min233ns,Max78.09ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -161,20 +161,20 @@ => CIGAR.Insertions 7.37 Kbases ( 4.18 %) (samples=7K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 5.44 Kbases ( 3.09 %) (samples=5K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.p0.alg -a gap-affine-wfa --check=correct --affine-penalties=0,1,2,1" - User time (seconds): 0.41 - System time (seconds): 0.06 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.47 + User time (seconds): 0.50 + System time (seconds): 0.05 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.56 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 130052 + Maximum resident set size (kbytes): 130228 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 31986 + Minor (reclaiming a frame) page faults: 31988 Voluntary context switches: 1 - Involuntary context switches: 0 + Involuntary context switches: 8 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -185,8 +185,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 669.98 ms ( 1 call, 669.98 ms/call {min669.98ms,Max669.98ms}) - => Time.Alignment 661.48 ms ( 98.73 %) ( 305 calls, 2.17 ms/call {min221ns,Max91.45ms}) +=> Time.Benchmark 603.01 ms ( 1 call, 603.01 ms/call {min603.01ms,Max603.01ms}) + => Time.Alignment 594.56 ms ( 98.60 %) ( 305 calls, 1.95 ms/call {min214ns,Max91.47ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -198,20 +198,20 @@ => CIGAR.Insertions 8.82 Kbases ( 5.00 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.90 Kbases ( 3.91 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.p1.alg -a gap-affine-wfa --check=correct --affine-penalties=0,3,1,4" - User time (seconds): 0.61 - System time (seconds): 0.06 + User time (seconds): 0.55 + System time (seconds): 0.05 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.67 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.61 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 158424 + Maximum resident set size (kbytes): 158504 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 39084 + Minor (reclaiming a frame) page faults: 39089 Voluntary context switches: 1 - Involuntary context switches: 6 + Involuntary context switches: 2 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -222,8 +222,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.48 s ( 1 call, 1.48 s/call {min1.48s,Max1.48s}) - => Time.Alignment 1.47 s ( 99.41 %) ( 305 calls, 4.83 ms/call {min212ns,Max238.23ms}) +=> Time.Benchmark 1.49 s ( 1 call, 1.49 s/call {min1.49s,Max1.49s}) + => Time.Alignment 1.49 s ( 99.45 %) ( 305 calls, 4.87 ms/call {min217ns,Max235.63ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -235,20 +235,20 @@ => CIGAR.Insertions 10.89 Kbases ( 6.18 %) (samples=10K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 8.97 Kbases ( 5.09 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.p2.alg -a gap-affine-wfa --check=correct --affine-penalties=0,5,3,2" - User time (seconds): 1.40 - System time (seconds): 0.09 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.49 + User time (seconds): 1.39 + System time (seconds): 0.10 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.50 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 367312 + Maximum resident set size (kbytes): 367252 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 91255 Voluntary context switches: 1 - Involuntary context switches: 5 + Involuntary context switches: 13 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -259,8 +259,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.92 s ( 1 call, 1.92 s/call {min1.92s,Max1.92s}) - => Time.Alignment 1.91 s ( 99.52 %) ( 305 calls, 6.26 ms/call {min221ns,Max316.14ms}) +=> Time.Benchmark 1.90 s ( 1 call, 1.90 s/call {min1.90s,Max1.90s}) + => Time.Alignment 1.89 s ( 99.38 %) ( 305 calls, 6.20 ms/call {min216ns,Max329.75ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -272,20 +272,20 @@ => CIGAR.Insertions 11.19 Kbases ( 6.34 %) (samples=11K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 9.26 Kbases ( 5.25 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.p3.alg -a gap-affine-wfa --check=correct --affine-penalties=-5,1,2,1" - User time (seconds): 1.76 - System time (seconds): 0.16 + User time (seconds): 1.71 + System time (seconds): 0.20 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.93 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.92 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 566324 + Maximum resident set size (kbytes): 566172 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 141033 + Minor (reclaiming a frame) page faults: 141030 Voluntary context switches: 1 - Involuntary context switches: 4 + Involuntary context switches: 15 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -296,8 +296,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 851.06 ms ( 1 call, 851.06 ms/call {min851.06ms,Max851.06ms}) - => Time.Alignment 842.62 ms ( 99.01 %) ( 305 calls, 2.76 ms/call {min218ns,Max125.18ms}) +=> Time.Benchmark 880.78 ms ( 1 call, 880.78 ms/call {min880.78ms,Max880.78ms}) + => Time.Alignment 871.04 ms ( 98.89 %) ( 305 calls, 2.86 ms/call {min221ns,Max125.47ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -309,20 +309,20 @@ => CIGAR.Insertions 9.74 Kbases ( 5.52 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 7.82 Kbases ( 4.43 %) (samples=7K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.p4.alg -a gap-affine-wfa --check=correct --affine-penalties=-2,3,1,4" - User time (seconds): 0.79 + User time (seconds): 0.82 System time (seconds): 0.06 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.86 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.89 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 218400 + Maximum resident set size (kbytes): 218324 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 54046 + Minor (reclaiming a frame) page faults: 54045 Voluntary context switches: 1 - Involuntary context switches: 1 + Involuntary context switches: 7 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -333,8 +333,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 2.82 s ( 1 call, 2.82 s/call {min2.82s,Max2.82s}) - => Time.Alignment 2.81 s ( 99.67 %) ( 305 calls, 9.22 ms/call {min245ns,Max505.26ms}) +=> Time.Benchmark 2.70 s ( 1 call, 2.70 s/call {min2.70s,Max2.70s}) + => Time.Alignment 2.69 s ( 99.66 %) ( 305 calls, 8.83 ms/call {min225ns,Max464.88ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -346,20 +346,20 @@ => CIGAR.Insertions 11.45 Kbases ( 6.49 %) (samples=11K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 9.53 Kbases ( 5.40 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.p5.alg -a gap-affine-wfa --check=correct --affine-penalties=-3,5,3,2" - User time (seconds): 2.58 - System time (seconds): 0.26 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.85 + User time (seconds): 2.48 + System time (seconds): 0.24 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.73 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 827592 + Maximum resident set size (kbytes): 827548 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 206352 Voluntary context switches: 1 - Involuntary context switches: 16 + Involuntary context switches: 18 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -370,8 +370,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 109.99 ms ( 1 call, 109.99 ms/call {min109.99ms,Max109.99ms}) - => Time.Alignment 101.57 ms ( 92.35 %) ( 305 calls, 333.01 us/call {min232ns,Max27.82ms}) +=> Time.Benchmark 136.90 ms ( 1 call, 136.90 ms/call {min136.90ms,Max136.90ms}) + => Time.Alignment 125.09 ms ( 91.37 %) ( 305 calls, 410.12 us/call {min228ns,Max24.86ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -383,18 +383,18 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.wfapt0.alg -a gap-affine-wfa --check=correct --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1" - User time (seconds): 0.09 - System time (seconds): 0.01 + User time (seconds): 0.11 + System time (seconds): 0.02 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.14 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 61084 + Maximum resident set size (kbytes): 61132 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 14716 + Minor (reclaiming a frame) page faults: 14717 Voluntary context switches: 1 Involuntary context switches: 1 Swaps: 0 @@ -407,8 +407,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 878.06 ms ( 1 call, 878.06 ms/call {min878.06ms,Max878.06ms}) - => Time.Alignment 870.01 ms ( 99.08 %) ( 305 calls, 2.85 ms/call {min234ns,Max124.85ms}) +=> Time.Benchmark 806.19 ms ( 1 call, 806.19 ms/call {min806.19ms,Max806.19ms}) + => Time.Alignment 798.17 ms ( 99.01 %) ( 305 calls, 2.62 ms/call {min246ns,Max126.94ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -420,20 +420,20 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.affine.wfapt1.alg -a gap-affine-wfa --check=correct --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10" - User time (seconds): 0.81 - System time (seconds): 0.05 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.88 + User time (seconds): 0.76 + System time (seconds): 0.04 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.81 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 207428 + Maximum resident set size (kbytes): 207568 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 51352 Voluntary context switches: 1 - Involuntary context switches: 13 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -444,18 +444,18 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 110.24 ms ( 1 call, 110.24 ms/call {min110.24ms,Max110.24ms}) - => Time.Alignment 109.65 ms ( 99.47 %) ( 305 calls, 359.50 us/call {min233ns,Max14.31ms}) +=> Time.Benchmark 91.12 ms ( 1 call, 91.12 ms/call {min91.12ms,Max91.12ms}) + => Time.Alignment 90.78 ms ( 99.63 %) ( 305 calls, 297.63 us/call {min204ns,Max9.06ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.indel.alg -a indel-wfa --wfa-score-only" - User time (seconds): 0.11 + User time (seconds): 0.09 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.09 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 2756 + Maximum resident set size (kbytes): 2692 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 169 @@ -471,23 +471,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 99.08 ms ( 1 call, 99.08 ms/call {min99.08ms,Max99.08ms}) - => Time.Alignment 98.32 ms ( 99.24 %) ( 305 calls, 322.38 us/call {min221ns,Max13.58ms}) +=> Time.Benchmark 97.04 ms ( 1 call, 97.04 ms/call {min97.04ms,Max97.04ms}) + => Time.Alignment 96.61 ms ( 99.56 %) ( 305 calls, 316.75 us/call {min194ns,Max13.37ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.edit.alg -a edit-wfa --wfa-score-only" - User time (seconds): 0.10 + User time (seconds): 0.09 System time (seconds): 0.00 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.10 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.09 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 2736 + Maximum resident set size (kbytes): 2752 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 161 + Minor (reclaiming a frame) page faults: 162 Voluntary context switches: 1 - Involuntary context switches: 1 + Involuntary context switches: 0 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -498,23 +498,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 838.02 ms ( 1 call, 838.02 ms/call {min838.02ms,Max838.02ms}) - => Time.Alignment 837.48 ms ( 99.94 %) ( 305 calls, 2.75 ms/call {min207ns,Max83.53ms}) +=> Time.Benchmark 911.95 ms ( 1 call, 911.95 ms/call {min911.95ms,Max911.95ms}) + => Time.Alignment 911.41 ms ( 99.94 %) ( 305 calls, 2.99 ms/call {min210ns,Max119.30ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.alg -a gap-affine-wfa --wfa-score-only" - User time (seconds): 0.83 + User time (seconds): 0.90 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.83 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.91 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4576 + Maximum resident set size (kbytes): 4624 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 620 - Voluntary context switches: 1 - Involuntary context switches: 2 + Minor (reclaiming a frame) page faults: 622 + Voluntary context switches: 3 + Involuntary context switches: 10 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -525,23 +525,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 5.24 s ( 1 call, 5.24 s/call {min5.24s,Max5.24s}) - => Time.Alignment 5.24 s ( 99.99 %) ( 305 calls, 17.18 ms/call {min225ns,Max629.20ms}) +=> Time.Benchmark 4.74 s ( 1 call, 4.74 s/call {min4.74s,Max4.74s}) + => Time.Alignment 4.74 s ( 99.99 %) ( 305 calls, 15.54 ms/call {min223ns,Max475.39ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine2p.alg -a gap-affine2p-wfa --wfa-score-only" - User time (seconds): 5.23 + User time (seconds): 4.73 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:05.24 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.74 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 28140 + Maximum resident set size (kbytes): 28180 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 6473 + Minor (reclaiming a frame) page faults: 6475 Voluntary context switches: 1 - Involuntary context switches: 51 + Involuntary context switches: 20 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -552,23 +552,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 358.72 ms ( 1 call, 358.72 ms/call {min358.72ms,Max358.72ms}) - => Time.Alignment 358.32 ms ( 99.89 %) ( 305 calls, 1.17 ms/call {min225ns,Max37.69ms}) +=> Time.Benchmark 374.41 ms ( 1 call, 374.41 ms/call {min374.41ms,Max374.41ms}) + => Time.Alignment 373.91 ms ( 99.87 %) ( 305 calls, 1.23 ms/call {min206ns,Max36.87ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.p0.alg -a gap-affine-wfa --wfa-score-only --affine-penalties=0,1,2,1" - User time (seconds): 0.35 + User time (seconds): 0.37 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.35 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.37 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3728 + Maximum resident set size (kbytes): 3880 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 402 - Voluntary context switches: 1 - Involuntary context switches: 5 + Minor (reclaiming a frame) page faults: 406 + Voluntary context switches: 2 + Involuntary context switches: 2 Swaps: 0 File system inputs: 0 File system outputs: 16 @@ -579,23 +579,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 507.86 ms ( 1 call, 507.86 ms/call {min507.86ms,Max507.86ms}) - => Time.Alignment 507.29 ms ( 99.89 %) ( 305 calls, 1.66 ms/call {min214ns,Max52.11ms}) +=> Time.Benchmark 434.34 ms ( 1 call, 434.34 ms/call {min434.34ms,Max434.34ms}) + => Time.Alignment 433.91 ms ( 99.90 %) ( 305 calls, 1.42 ms/call {min206ns,Max41.64ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.p1.alg -a gap-affine-wfa --wfa-score-only --affine-penalties=0,3,1,4" - User time (seconds): 0.50 + User time (seconds): 0.43 System time (seconds): 0.00 Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.50 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.43 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3336 + Maximum resident set size (kbytes): 3300 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 303 - Voluntary context switches: 0 - Involuntary context switches: 1 + Minor (reclaiming a frame) page faults: 301 + Voluntary context switches: 1 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -606,21 +606,21 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.41 s ( 1 call, 1.41 s/call {min1.41s,Max1.41s}) - => Time.Alignment 1.41 s ( 99.91 %) ( 305 calls, 4.63 ms/call {min344ns,Max178.91ms}) +=> Time.Benchmark 1.17 s ( 1 call, 1.17 s/call {min1.17s,Max1.17s}) + => Time.Alignment 1.17 s ( 99.95 %) ( 305 calls, 3.82 ms/call {min202ns,Max113.40ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.p2.alg -a gap-affine-wfa --wfa-score-only --affine-penalties=0,5,3,2" - User time (seconds): 1.41 + User time (seconds): 1.16 System time (seconds): 0.00 Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.41 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.16 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4820 + Maximum resident set size (kbytes): 4780 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 701 + Minor (reclaiming a frame) page faults: 698 Voluntary context switches: 1 Involuntary context switches: 6 Swaps: 0 @@ -633,23 +633,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.49 s ( 1 call, 1.49 s/call {min1.49s,Max1.49s}) - => Time.Alignment 1.49 s ( 99.95 %) ( 305 calls, 4.89 ms/call {min206ns,Max161.17ms}) +=> Time.Benchmark 1.50 s ( 1 call, 1.50 s/call {min1.50s,Max1.50s}) + => Time.Alignment 1.50 s ( 99.97 %) ( 305 calls, 4.90 ms/call {min209ns,Max147.59ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.p3.alg -a gap-affine-wfa --wfa-score-only --affine-penalties=-5,1,2,1" - User time (seconds): 1.48 + User time (seconds): 1.49 System time (seconds): 0.00 - Percent of CPU this job got: 100% + Percent of CPU this job got: 99% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.49 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4812 + Maximum resident set size (kbytes): 4800 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 666 + Minor (reclaiming a frame) page faults: 667 Voluntary context switches: 1 - Involuntary context switches: 4 + Involuntary context switches: 10 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -660,23 +660,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 707.12 ms ( 1 call, 707.12 ms/call {min707.12ms,Max707.12ms}) - => Time.Alignment 706.62 ms ( 99.93 %) ( 305 calls, 2.32 ms/call {min210ns,Max68.17ms}) +=> Time.Benchmark 657.87 ms ( 1 call, 657.87 ms/call {min657.87ms,Max657.87ms}) + => Time.Alignment 657.26 ms ( 99.91 %) ( 305 calls, 2.15 ms/call {min214ns,Max61.01ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.p4.alg -a gap-affine-wfa --wfa-score-only --affine-penalties=-2,3,1,4" - User time (seconds): 0.70 + User time (seconds): 0.65 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.70 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.65 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3800 + Maximum resident set size (kbytes): 3820 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 417 + Minor (reclaiming a frame) page faults: 418 Voluntary context switches: 1 - Involuntary context switches: 3 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -687,23 +687,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 2.06 s ( 1 call, 2.06 s/call {min2.06s,Max2.06s}) - => Time.Alignment 2.06 s ( 99.97 %) ( 305 calls, 6.74 ms/call {min210ns,Max197.96ms}) +=> Time.Benchmark 2.09 s ( 1 call, 2.09 s/call {min2.09s,Max2.09s}) + => Time.Alignment 2.09 s ( 99.97 %) ( 305 calls, 6.86 ms/call {min219ns,Max196.95ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.p5.alg -a gap-affine-wfa --wfa-score-only --affine-penalties=-3,5,3,2" - User time (seconds): 2.05 + User time (seconds): 2.08 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.05 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.09 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 7060 + Maximum resident set size (kbytes): 6916 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1199 + Minor (reclaiming a frame) page faults: 1200 Voluntary context switches: 1 - Involuntary context switches: 7 + Involuntary context switches: 8 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -714,21 +714,21 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 51.04 ms ( 1 call, 51.04 ms/call {min51.04ms,Max51.04ms}) - => Time.Alignment 50.58 ms ( 99.10 %) ( 305 calls, 165.82 us/call {min204ns,Max4.08ms}) +=> Time.Benchmark 62.41 ms ( 1 call, 62.41 ms/call {min62.41ms,Max62.41ms}) + => Time.Alignment 61.84 ms ( 99.08 %) ( 305 calls, 202.74 us/call {min207ns,Max4.84ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.wfapt0.alg -a gap-affine-wfa --wfa-score-only --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1" - User time (seconds): 0.05 + User time (seconds): 0.06 System time (seconds): 0.00 Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.05 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.06 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 2744 + Maximum resident set size (kbytes): 2728 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 149 + Minor (reclaiming a frame) page faults: 147 Voluntary context switches: 1 Involuntary context switches: 0 Swaps: 0 @@ -741,23 +741,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 797.93 ms ( 1 call, 797.93 ms/call {min797.93ms,Max797.93ms}) - => Time.Alignment 797.23 ms ( 99.91 %) ( 305 calls, 2.61 ms/call {min319ns,Max109.81ms}) +=> Time.Benchmark 678.71 ms ( 1 call, 678.71 ms/call {min678.71ms,Max678.71ms}) + => Time.Alignment 678.05 ms ( 99.90 %) ( 305 calls, 2.22 ms/call {min234ns,Max83.40ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.score.affine.wfapt1.alg -a gap-affine-wfa --wfa-score-only --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10" - User time (seconds): 0.78 + User time (seconds): 0.67 System time (seconds): 0.00 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.80 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.68 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4156 + Maximum resident set size (kbytes): 4084 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 474 + Minor (reclaiming a frame) page faults: 470 Voluntary context switches: 1 - Involuntary context switches: 33 + Involuntary context switches: 6 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -768,8 +768,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 191.56 ms ( 1 call, 191.56 ms/call {min191.56ms,Max191.56ms}) - => Time.Alignment 177.13 ms ( 92.46 %) ( 305 calls, 580.74 us/call {min320ns,Max20.32ms}) +=> Time.Benchmark 163.49 ms ( 1 call, 163.49 ms/call {min163.49ms,Max163.49ms}) + => Time.Alignment 154.61 ms ( 94.57 %) ( 305 calls, 506.90 us/call {min240ns,Max40.97ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -781,20 +781,20 @@ => CIGAR.Insertions 19.08 Kbases ( 10.82 %) (samples=19K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 17.16 Kbases ( 9.73 %) (samples=17K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.indel.alg -a indel-wfa --wfa-memory-mode=med --check=correct" - User time (seconds): 0.18 - System time (seconds): 0.00 - Percent of CPU this job got: 97% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.19 + User time (seconds): 0.14 + System time (seconds): 0.01 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.16 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4284 + Maximum resident set size (kbytes): 4184 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 542 + Minor (reclaiming a frame) page faults: 539 Voluntary context switches: 1 - Involuntary context switches: 7 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 248 @@ -805,8 +805,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 122.31 ms ( 1 call, 122.31 ms/call {min122.31ms,Max122.31ms}) - => Time.Alignment 112.76 ms ( 92.19 %) ( 305 calls, 369.70 us/call {min250ns,Max11.90ms}) +=> Time.Benchmark 113.84 ms ( 1 call, 113.84 ms/call {min113.84ms,Max113.84ms}) + => Time.Alignment 105.67 ms ( 92.83 %) ( 305 calls, 346.45 us/call {min239ns,Max11.12ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -818,20 +818,20 @@ => CIGAR.Insertions 10.30 Kbases ( 5.84 %) (samples=10K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 8.38 Kbases ( 4.75 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.edit.alg -a edit-wfa --wfa-memory-mode=med --check=correct" - User time (seconds): 0.12 + User time (seconds): 0.11 System time (seconds): 0.00 Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.12 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4004 + Maximum resident set size (kbytes): 4028 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 486 + Minor (reclaiming a frame) page faults: 487 Voluntary context switches: 1 - Involuntary context switches: 5 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -842,8 +842,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 2.44 s ( 1 call, 2.44 s/call {min2.44s,Max2.44s}) - => Time.Alignment 2.43 s ( 99.61 %) ( 305 calls, 7.95 ms/call {min250ns,Max324.53ms}) +=> Time.Benchmark 2.30 s ( 1 call, 2.30 s/call {min2.30s,Max2.30s}) + => Time.Alignment 2.29 s ( 99.64 %) ( 305 calls, 7.50 ms/call {min307ns,Max246.06ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -855,20 +855,20 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct" - User time (seconds): 2.39 + User time (seconds): 2.25 System time (seconds): 0.04 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.43 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.30 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 72888 + Maximum resident set size (kbytes): 72948 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 17805 + Minor (reclaiming a frame) page faults: 17807 Voluntary context switches: 1 - Involuntary context switches: 33 + Involuntary context switches: 9 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -879,8 +879,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 20.97 s ( 1 call, 20.97 s/call {min20.97s,Max20.97s}) - => Time.Alignment 20.96 s ( 99.95 %) ( 305 calls, 68.73 ms/call {min274ns,Max2.65s}) +=> Time.Benchmark 15.04 s ( 1 call, 15.04 s/call {min15.04s,Max15.04s}) + => Time.Alignment 15.03 s ( 99.94 %) ( 305 calls, 49.29 ms/call {min269ns,Max1.60s}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -892,20 +892,20 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine2p.alg -a gap-affine2p-wfa --wfa-memory-mode=med --check=correct" - User time (seconds): 20.54 - System time (seconds): 0.25 + User time (seconds): 14.93 + System time (seconds): 0.11 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:20.98 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:15.05 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 414816 + Maximum resident set size (kbytes): 414788 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 104226 + Minor (reclaiming a frame) page faults: 104225 Voluntary context switches: 1 - Involuntary context switches: 348 + Involuntary context switches: 77 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -916,8 +916,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.01 s ( 1 call, 1.01 s/call {min1.01s,Max1.01s}) - => Time.Alignment 998.14 ms ( 99.10 %) ( 305 calls, 3.27 ms/call {min256ns,Max105.58ms}) +=> Time.Benchmark 976.50 ms ( 1 call, 976.50 ms/call {min976.50ms,Max976.50ms}) + => Time.Alignment 968.40 ms ( 99.17 %) ( 305 calls, 3.18 ms/call {min267ns,Max102.07ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -929,20 +929,20 @@ => CIGAR.Insertions 7.37 Kbases ( 4.18 %) (samples=7K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 5.44 Kbases ( 3.09 %) (samples=5K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.p0.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --affine-penalties=0,1,2,1" - User time (seconds): 1.00 - System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.00 + User time (seconds): 0.96 + System time (seconds): 0.01 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.97 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 30844 + Maximum resident set size (kbytes): 30748 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 7253 + Minor (reclaiming a frame) page faults: 7254 Voluntary context switches: 1 - Involuntary context switches: 6 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 184 @@ -953,8 +953,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 913.73 ms ( 1 call, 913.73 ms/call {min913.73ms,Max913.73ms}) - => Time.Alignment 904.89 ms ( 99.03 %) ( 305 calls, 2.97 ms/call {min255ns,Max91.44ms}) +=> Time.Benchmark 903.54 ms ( 1 call, 903.54 ms/call {min903.54ms,Max903.54ms}) + => Time.Alignment 894.83 ms ( 99.04 %) ( 305 calls, 2.93 ms/call {min276ns,Max90.94ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -966,20 +966,20 @@ => CIGAR.Insertions 8.82 Kbases ( 5.00 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.90 Kbases ( 3.91 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.p1.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --affine-penalties=0,3,1,4" - User time (seconds): 0.89 + User time (seconds): 0.88 System time (seconds): 0.02 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.91 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.90 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 32300 + Maximum resident set size (kbytes): 32220 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 7541 Voluntary context switches: 1 - Involuntary context switches: 8 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -990,8 +990,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 2.68 s ( 1 call, 2.68 s/call {min2.68s,Max2.68s}) - => Time.Alignment 2.67 s ( 99.70 %) ( 305 calls, 8.76 ms/call {min252ns,Max285.46ms}) +=> Time.Benchmark 2.77 s ( 1 call, 2.77 s/call {min2.77s,Max2.77s}) + => Time.Alignment 2.76 s ( 99.69 %) ( 305 calls, 9.06 ms/call {min252ns,Max280.42ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1003,20 +1003,20 @@ => CIGAR.Insertions 10.89 Kbases ( 6.18 %) (samples=10K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 8.97 Kbases ( 5.09 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.p2.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --affine-penalties=0,5,3,2" - User time (seconds): 2.67 - System time (seconds): 0.01 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.68 + User time (seconds): 2.73 + System time (seconds): 0.04 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.77 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 91308 + Maximum resident set size (kbytes): 91312 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 22459 + Minor (reclaiming a frame) page faults: 22461 Voluntary context switches: 1 - Involuntary context switches: 8 + Involuntary context switches: 18 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -1027,8 +1027,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 2.90 s ( 1 call, 2.90 s/call {min2.90s,Max2.90s}) - => Time.Alignment 2.89 s ( 99.70 %) ( 305 calls, 9.49 ms/call {min255ns,Max290.13ms}) +=> Time.Benchmark 2.87 s ( 1 call, 2.87 s/call {min2.87s,Max2.87s}) + => Time.Alignment 2.86 s ( 99.69 %) ( 305 calls, 9.38 ms/call {min266ns,Max291.94ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1040,20 +1040,20 @@ => CIGAR.Insertions 11.19 Kbases ( 6.34 %) (samples=11K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 9.26 Kbases ( 5.25 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.p3.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --affine-penalties=-5,1,2,1" - User time (seconds): 2.88 - System time (seconds): 0.01 + User time (seconds): 2.86 + System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.90 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.87 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 61044 + Maximum resident set size (kbytes): 61116 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 14859 Voluntary context switches: 1 - Involuntary context switches: 12 + Involuntary context switches: 8 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -1064,8 +1064,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.59 s ( 1 call, 1.59 s/call {min1.59s,Max1.59s}) - => Time.Alignment 1.58 s ( 99.47 %) ( 305 calls, 5.19 ms/call {min255ns,Max162.39ms}) +=> Time.Benchmark 1.61 s ( 1 call, 1.61 s/call {min1.61s,Max1.61s}) + => Time.Alignment 1.60 s ( 99.48 %) ( 305 calls, 5.26 ms/call {min255ns,Max160.36ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1077,20 +1077,20 @@ => CIGAR.Insertions 9.74 Kbases ( 5.52 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 7.82 Kbases ( 4.43 %) (samples=7K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.p4.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --affine-penalties=-2,3,1,4" - User time (seconds): 1.56 - System time (seconds): 0.02 + User time (seconds): 1.59 + System time (seconds): 0.01 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.59 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.61 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 43932 + Maximum resident set size (kbytes): 43948 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 10559 + Minor (reclaiming a frame) page faults: 10560 Voluntary context switches: 1 - Involuntary context switches: 12 + Involuntary context switches: 11 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -1101,8 +1101,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 4.31 s ( 1 call, 4.31 s/call {min4.31s,Max4.31s}) - => Time.Alignment 4.30 s ( 99.81 %) ( 305 calls, 14.11 ms/call {min261ns,Max439.51ms}) +=> Time.Benchmark 4.27 s ( 1 call, 4.27 s/call {min4.27s,Max4.27s}) + => Time.Alignment 4.26 s ( 99.80 %) ( 305 calls, 13.96 ms/call {min257ns,Max433.15ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1114,20 +1114,20 @@ => CIGAR.Insertions 11.45 Kbases ( 6.49 %) (samples=11K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 9.53 Kbases ( 5.40 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.p5.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --affine-penalties=-3,5,3,2" - User time (seconds): 4.27 - System time (seconds): 0.03 + User time (seconds): 4.24 + System time (seconds): 0.02 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.31 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:04.27 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 89776 + Maximum resident set size (kbytes): 89692 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 22158 + Minor (reclaiming a frame) page faults: 22157 Voluntary context switches: 1 - Involuntary context switches: 12 + Involuntary context switches: 17 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -1138,8 +1138,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 117.32 ms ( 1 call, 117.32 ms/call {min117.32ms,Max117.32ms}) - => Time.Alignment 108.24 ms ( 92.26 %) ( 305 calls, 354.88 us/call {min254ns,Max7.45ms}) +=> Time.Benchmark 99.32 ms ( 1 call, 99.32 ms/call {min99.32ms,Max99.32ms}) + => Time.Alignment 91.22 ms ( 91.84 %) ( 305 calls, 299.07 us/call {min268ns,Max6.01ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1151,18 +1151,18 @@ => CIGAR.Insertions 8.72 Kbases ( 4.95 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.wfapt0.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1" - User time (seconds): 0.10 + User time (seconds): 0.09 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.10 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3884 + Maximum resident set size (kbytes): 3748 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 434 + Minor (reclaiming a frame) page faults: 435 Voluntary context switches: 1 Involuntary context switches: 1 Swaps: 0 @@ -1176,7 +1176,7 @@ [Benchmark] => Total.reads 305 => Time.Benchmark 1.70 s ( 1 call, 1.70 s/call {min1.70s,Max1.70s}) - => Time.Alignment 1.69 s ( 99.52 %) ( 305 calls, 5.54 ms/call {min267ns,Max175.31ms}) + => Time.Alignment 1.69 s ( 99.52 %) ( 305 calls, 5.55 ms/call {min255ns,Max176.17ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1189,19 +1189,19 @@ => CIGAR.Deletions 6.80 Kbases ( 3.86 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.pb.affine.wfapt1.alg -a gap-affine-wfa --wfa-memory-mode=med --check=correct --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10" User time (seconds): 1.69 - System time (seconds): 0.00 + System time (seconds): 0.01 Percent of CPU this job got: 99% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.70 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 49012 + Maximum resident set size (kbytes): 49076 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 11774 + Minor (reclaiming a frame) page faults: 11773 Voluntary context switches: 1 - Involuntary context switches: 8 + Involuntary context switches: 11 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -1212,8 +1212,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 124.36 ms ( 1 call, 124.36 ms/call {min124.36ms,Max124.36ms}) - => Time.Alignment 114.39 ms ( 91.98 %) ( 305 calls, 375.03 us/call {min703ns,Max12.04ms}) +=> Time.Benchmark 117.36 ms ( 1 call, 117.36 ms/call {min117.36ms,Max117.36ms}) + => Time.Alignment 108.31 ms ( 92.29 %) ( 305 calls, 355.13 us/call {min697ns,Max11.38ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1227,18 +1227,18 @@ Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.indel.alg -a indel-wfa --wfa-memory-mode=ultralow --check=correct" User time (seconds): 0.11 System time (seconds): 0.00 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.12 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.11 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3404 + Maximum resident set size (kbytes): 3472 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 325 + Minor (reclaiming a frame) page faults: 328 Voluntary context switches: 1 - Involuntary context switches: 0 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 248 @@ -1249,8 +1249,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 107.42 ms ( 1 call, 107.42 ms/call {min107.42ms,Max107.42ms}) - => Time.Alignment 99.49 ms ( 92.62 %) ( 305 calls, 326.19 us/call {min695ns,Max10.01ms}) +=> Time.Benchmark 141.43 ms ( 1 call, 141.43 ms/call {min141.43ms,Max141.43ms}) + => Time.Alignment 133.59 ms ( 94.46 %) ( 305 calls, 437.99 us/call {min698ns,Max30.00ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1262,20 +1262,20 @@ => CIGAR.Insertions 10.30 Kbases ( 5.84 %) (samples=10K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 8.38 Kbases ( 4.75 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.edit.alg -a edit-wfa --wfa-memory-mode=ultralow --check=correct" - User time (seconds): 0.10 + User time (seconds): 0.13 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.10 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.14 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3472 + Maximum resident set size (kbytes): 3324 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 329 Voluntary context switches: 1 - Involuntary context switches: 0 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -1286,8 +1286,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.17 s ( 1 call, 1.17 s/call {min1.17s,Max1.17s}) - => Time.Alignment 1.16 s ( 99.30 %) ( 305 calls, 3.80 ms/call {min751ns,Max108.06ms}) +=> Time.Benchmark 1.15 s ( 1 call, 1.15 s/call {min1.15s,Max1.15s}) + => Time.Alignment 1.14 s ( 99.27 %) ( 305 calls, 3.73 ms/call {min704ns,Max113.02ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1299,20 +1299,20 @@ => CIGAR.Insertions 8.70 Kbases ( 4.93 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.77 Kbases ( 3.84 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct" - User time (seconds): 1.16 + User time (seconds): 1.14 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.16 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.14 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 5204 + Maximum resident set size (kbytes): 5080 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 750 + Minor (reclaiming a frame) page faults: 746 Voluntary context switches: 1 - Involuntary context switches: 6 + Involuntary context switches: 4 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -1323,8 +1323,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 7.35 s ( 1 call, 7.35 s/call {min7.35s,Max7.35s}) - => Time.Alignment 7.35 s ( 99.89 %) ( 305 calls, 24.08 ms/call {min755ns,Max696.67ms}) +=> Time.Benchmark 7.74 s ( 1 call, 7.74 s/call {min7.74s,Max7.74s}) + => Time.Alignment 7.73 s ( 99.87 %) ( 305 calls, 25.36 ms/call {min746ns,Max872.67ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1336,20 +1336,20 @@ => CIGAR.Insertions 8.70 Kbases ( 4.93 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.77 Kbases ( 3.84 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine2p.alg -a gap-affine2p-wfa --wfa-memory-mode=ultralow --check=correct" - User time (seconds): 7.34 - System time (seconds): 0.01 + User time (seconds): 7.70 + System time (seconds): 0.03 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.35 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:07.74 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 37012 + Maximum resident set size (kbytes): 37140 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 8767 - Voluntary context switches: 1 - Involuntary context switches: 41 + Minor (reclaiming a frame) page faults: 8769 + Voluntary context switches: 3 + Involuntary context switches: 55 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -1360,8 +1360,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 461.48 ms ( 1 call, 461.48 ms/call {min461.48ms,Max461.48ms}) - => Time.Alignment 453.19 ms ( 98.20 %) ( 305 calls, 1.49 ms/call {min740ns,Max47.46ms}) +=> Time.Benchmark 446.05 ms ( 1 call, 446.05 ms/call {min446.05ms,Max446.05ms}) + => Time.Alignment 438.20 ms ( 98.24 %) ( 305 calls, 1.44 ms/call {min750ns,Max43.89ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1373,20 +1373,20 @@ => CIGAR.Insertions 7.36 Kbases ( 4.17 %) (samples=7K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 5.43 Kbases ( 3.08 %) (samples=5K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.p0.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --affine-penalties=0,1,2,1" - User time (seconds): 0.46 + User time (seconds): 0.44 System time (seconds): 0.00 Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.46 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.44 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4880 + Maximum resident set size (kbytes): 4920 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 720 Voluntary context switches: 1 - Involuntary context switches: 3 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -1397,8 +1397,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 619.28 ms ( 1 call, 619.28 ms/call {min619.28ms,Max619.28ms}) - => Time.Alignment 611.32 ms ( 98.72 %) ( 305 calls, 2.00 ms/call {min725ns,Max57.22ms}) +=> Time.Benchmark 639.22 ms ( 1 call, 639.22 ms/call {min639.22ms,Max639.22ms}) + => Time.Alignment 630.97 ms ( 98.71 %) ( 305 calls, 2.07 ms/call {min739ns,Max68.64ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1410,20 +1410,20 @@ => CIGAR.Insertions 8.81 Kbases ( 4.99 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.88 Kbases ( 3.90 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.p1.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --affine-penalties=0,3,1,4" - User time (seconds): 0.61 + User time (seconds): 0.63 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.62 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.64 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4948 + Maximum resident set size (kbytes): 4936 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 684 + Minor (reclaiming a frame) page faults: 682 Voluntary context switches: 1 - Involuntary context switches: 2 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -1434,8 +1434,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.51 s ( 1 call, 1.51 s/call {min1.51s,Max1.51s}) - => Time.Alignment 1.50 s ( 99.33 %) ( 305 calls, 4.91 ms/call {min709ns,Max142.09ms}) +=> Time.Benchmark 1.52 s ( 1 call, 1.52 s/call {min1.52s,Max1.52s}) + => Time.Alignment 1.51 s ( 99.45 %) ( 305 calls, 4.95 ms/call {min734ns,Max155.30ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1447,20 +1447,20 @@ => CIGAR.Insertions 10.91 Kbases ( 6.19 %) (samples=10K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 8.99 Kbases ( 5.10 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.p2.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --affine-penalties=0,5,3,2" - User time (seconds): 1.50 + User time (seconds): 1.51 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.51 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.52 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 5908 + Maximum resident set size (kbytes): 6032 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 986 - Voluntary context switches: 2 - Involuntary context switches: 5 + Minor (reclaiming a frame) page faults: 989 + Voluntary context switches: 1 + Involuntary context switches: 11 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -1471,8 +1471,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.95 s ( 1 call, 1.95 s/call {min1.95s,Max1.95s}) - => Time.Alignment 1.94 s ( 99.59 %) ( 305 calls, 6.35 ms/call {min751ns,Max168.61ms}) +=> Time.Benchmark 1.92 s ( 1 call, 1.92 s/call {min1.92s,Max1.92s}) + => Time.Alignment 1.91 s ( 99.57 %) ( 305 calls, 6.25 ms/call {min751ns,Max174.22ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1484,20 +1484,20 @@ => CIGAR.Insertions 11.18 Kbases ( 6.34 %) (samples=11K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 9.26 Kbases ( 5.25 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.p3.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --affine-penalties=-5,1,2,1" - User time (seconds): 1.94 + User time (seconds): 1.91 System time (seconds): 0.00 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.94 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.91 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 6364 + Maximum resident set size (kbytes): 6516 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 1097 Voluntary context switches: 1 - Involuntary context switches: 8 + Involuntary context switches: 4 Swaps: 0 File system inputs: 0 File system outputs: 208 @@ -1508,8 +1508,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 969.63 ms ( 1 call, 969.63 ms/call {min969.63ms,Max969.63ms}) - => Time.Alignment 960.99 ms ( 99.11 %) ( 305 calls, 3.15 ms/call {min736ns,Max87.93ms}) +=> Time.Benchmark 989.03 ms ( 1 call, 989.03 ms/call {min989.03ms,Max989.03ms}) + => Time.Alignment 980.50 ms ( 99.14 %) ( 305 calls, 3.21 ms/call {min730ns,Max91.71ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1521,20 +1521,20 @@ => CIGAR.Insertions 9.74 Kbases ( 5.52 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 7.81 Kbases ( 4.43 %) (samples=7K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.p4.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --affine-penalties=-2,3,1,4" - User time (seconds): 0.97 + User time (seconds): 0.99 System time (seconds): 0.00 Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.97 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.99 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4148 + Maximum resident set size (kbytes): 4260 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 528 + Minor (reclaiming a frame) page faults: 529 Voluntary context switches: 1 - Involuntary context switches: 3 + Involuntary context switches: 2 Swaps: 0 File system inputs: 0 File system outputs: 200 @@ -1545,8 +1545,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 2.94 s ( 1 call, 2.94 s/call {min2.94s,Max2.94s}) - => Time.Alignment 2.93 s ( 99.65 %) ( 305 calls, 9.61 ms/call {min738ns,Max263.79ms}) +=> Time.Benchmark 2.90 s ( 1 call, 2.90 s/call {min2.90s,Max2.90s}) + => Time.Alignment 2.89 s ( 99.70 %) ( 305 calls, 9.46 ms/call {min756ns,Max274.54ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1558,23 +1558,23 @@ => CIGAR.Insertions 11.45 Kbases ( 6.49 %) (samples=11K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 9.53 Kbases ( 5.40 %) (samples=9K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.p5.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --affine-penalties=-3,5,3,2" - User time (seconds): 2.93 + User time (seconds): 2.89 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.94 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.89 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 7168 + Maximum resident set size (kbytes): 7292 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1263 - Voluntary context switches: 3 - Involuntary context switches: 10 + Minor (reclaiming a frame) page faults: 1265 + Voluntary context switches: 1 + Involuntary context switches: 14 Swaps: 0 File system inputs: 0 - File system outputs: 208 + File system outputs: 200 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 @@ -1582,8 +1582,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 317.33 ms ( 1 call, 317.33 ms/call {min317.33ms,Max317.33ms}) - => Time.Alignment 308.70 ms ( 97.28 %) ( 305 calls, 1.01 ms/call {min726ns,Max22.24ms}) +=> Time.Benchmark 347.59 ms ( 1 call, 347.59 ms/call {min347.59ms,Max347.59ms}) + => Time.Alignment 336.67 ms ( 96.86 %) ( 305 calls, 1.10 ms/call {min740ns,Max34.92ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1595,23 +1595,23 @@ => CIGAR.Insertions 8.70 Kbases ( 4.93 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.77 Kbases ( 3.84 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.wfapt0.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1" - User time (seconds): 0.31 - System time (seconds): 0.00 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.31 + User time (seconds): 0.33 + System time (seconds): 0.01 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.34 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3620 + Maximum resident set size (kbytes): 3532 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 365 + Minor (reclaiming a frame) page faults: 367 Voluntary context switches: 1 - Involuntary context switches: 3 + Involuntary context switches: 7 Swaps: 0 File system inputs: 0 - File system outputs: 192 + File system outputs: 200 Socket messages sent: 0 Socket messages received: 0 Signals delivered: 0 @@ -1619,8 +1619,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 873.04 ms ( 1 call, 873.04 ms/call {min873.04ms,Max873.04ms}) - => Time.Alignment 864.87 ms ( 99.06 %) ( 305 calls, 2.84 ms/call {min711ns,Max82.97ms}) +=> Time.Benchmark 1.04 s ( 1 call, 1.04 s/call {min1.04s,Max1.04s}) + => Time.Alignment 936.48 ms ( 89.95 %) ( 305 calls, 3.07 ms/call {min735ns,Max90.35ms}) [Accuracy] => Alignments.Correct 305.00 alg (100.00 %) (samples=305{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => Score.Correct 0.00 alg ( 0.00 %) (samples=0,--n/a--)} @@ -1632,20 +1632,20 @@ => CIGAR.Insertions 8.70 Kbases ( 4.93 %) (samples=8K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} => CIGAR.Deletions 6.77 Kbases ( 3.84 %) (samples=6K{mean1.00,min1.00,Max1.00,Var0.00,StdDev0.00)} Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.affine.wfapt1.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --check=correct --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10" - User time (seconds): 0.87 + User time (seconds): 0.94 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.87 + Percent of CPU this job got: 90% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.04 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4604 + Maximum resident set size (kbytes): 4688 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 625 - Voluntary context switches: 1 - Involuntary context switches: 2 + Minor (reclaiming a frame) page faults: 628 + Voluntary context switches: 2 + Involuntary context switches: 5 Swaps: 0 File system inputs: 0 File system outputs: 192 @@ -1656,8 +1656,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 54.32 ms ( 1 call, 54.32 ms/call {min54.32ms,Max54.32ms}) - => Time.Alignment 53.86 ms ( 99.16 %) ( 305 calls, 176.59 us/call {min528ns,Max5.79ms}) +=> Time.Benchmark 54.13 ms ( 1 call, 54.13 ms/call {min54.13ms,Max54.13ms}) + => Time.Alignment 53.69 ms ( 99.18 %) ( 305 calls, 176.03 us/call {min510ns,Max5.48ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.indel.alg -a indel-wfa --wfa-memory-mode=ultralow --wfa-score-only" User time (seconds): 0.05 System time (seconds): 0.00 @@ -1667,7 +1667,7 @@ Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3108 + Maximum resident set size (kbytes): 3104 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 209 @@ -1683,23 +1683,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 92.72 ms ( 1 call, 92.72 ms/call {min92.72ms,Max92.72ms}) - => Time.Alignment 92.04 ms ( 99.28 %) ( 305 calls, 301.78 us/call {min509ns,Max13.69ms}) +=> Time.Benchmark 51.68 ms ( 1 call, 51.68 ms/call {min51.68ms,Max51.68ms}) + => Time.Alignment 51.19 ms ( 99.04 %) ( 305 calls, 167.83 us/call {min503ns,Max5.73ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.edit.alg -a edit-wfa --wfa-memory-mode=ultralow --wfa-score-only" - User time (seconds): 0.09 + User time (seconds): 0.04 System time (seconds): 0.00 - Percent of CPU this job got: 97% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.09 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.05 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 2956 + Maximum resident set size (kbytes): 3088 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 210 + Minor (reclaiming a frame) page faults: 209 Voluntary context switches: 1 - Involuntary context switches: 4 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1710,23 +1710,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 541.29 ms ( 1 call, 541.29 ms/call {min541.29ms,Max541.29ms}) - => Time.Alignment 540.73 ms ( 99.90 %) ( 305 calls, 1.77 ms/call {min505ns,Max59.99ms}) +=> Time.Benchmark 537.96 ms ( 1 call, 537.96 ms/call {min537.96ms,Max537.96ms}) + => Time.Alignment 537.13 ms ( 99.85 %) ( 305 calls, 1.76 ms/call {min1.00us,Max54.54ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only" - User time (seconds): 0.54 + User time (seconds): 0.53 System time (seconds): 0.00 - Percent of CPU this job got: 100% + Percent of CPU this job got: 99% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.54 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4280 + Maximum resident set size (kbytes): 4416 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 580 Voluntary context switches: 1 - Involuntary context switches: 2 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1737,23 +1737,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 3.02 s ( 1 call, 3.02 s/call {min3.02s,Max3.02s}) - => Time.Alignment 3.02 s ( 99.98 %) ( 305 calls, 9.90 ms/call {min561ns,Max290.97ms}) +=> Time.Benchmark 2.97 s ( 1 call, 2.97 s/call {min2.97s,Max2.97s}) + => Time.Alignment 2.97 s ( 99.98 %) ( 305 calls, 9.74 ms/call {min569ns,Max289.46ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine2p.alg -a gap-affine2p-wfa --wfa-memory-mode=ultralow --wfa-score-only" - User time (seconds): 3.00 + User time (seconds): 2.95 System time (seconds): 0.01 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:03.02 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:02.97 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 35208 + Maximum resident set size (kbytes): 35232 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 8268 + Minor (reclaiming a frame) page faults: 8266 Voluntary context switches: 1 - Involuntary context switches: 14 + Involuntary context switches: 9 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1764,21 +1764,21 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 215.07 ms ( 1 call, 215.07 ms/call {min215.07ms,Max215.07ms}) - => Time.Alignment 214.62 ms ( 99.79 %) ( 305 calls, 703.66 us/call {min551ns,Max23.07ms}) +=> Time.Benchmark 215.62 ms ( 1 call, 215.62 ms/call {min215.62ms,Max215.62ms}) + => Time.Alignment 215.19 ms ( 99.80 %) ( 305 calls, 705.54 us/call {min509ns,Max21.84ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.p0.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --affine-penalties=0,1,2,1" - User time (seconds): 0.20 + User time (seconds): 0.21 System time (seconds): 0.00 - Percent of CPU this job got: 99% + Percent of CPU this job got: 100% Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.21 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3616 + Maximum resident set size (kbytes): 3608 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 395 + Minor (reclaiming a frame) page faults: 397 Voluntary context switches: 1 Involuntary context switches: 0 Swaps: 0 @@ -1791,23 +1791,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 344.29 ms ( 1 call, 344.29 ms/call {min344.29ms,Max344.29ms}) - => Time.Alignment 343.86 ms ( 99.87 %) ( 305 calls, 1.13 ms/call {min508ns,Max45.25ms}) +=> Time.Benchmark 295.73 ms ( 1 call, 295.73 ms/call {min295.73ms,Max295.73ms}) + => Time.Alignment 295.11 ms ( 99.79 %) ( 305 calls, 967.57 us/call {min511ns,Max35.70ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.p1.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --affine-penalties=0,3,1,4" - User time (seconds): 0.34 + User time (seconds): 0.29 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.34 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.29 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3488 + Maximum resident set size (kbytes): 3512 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 372 - Voluntary context switches: 1 - Involuntary context switches: 12 + Minor (reclaiming a frame) page faults: 369 + Voluntary context switches: 2 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1818,21 +1818,21 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 665.26 ms ( 1 call, 665.26 ms/call {min665.26ms,Max665.26ms}) - => Time.Alignment 664.69 ms ( 99.91 %) ( 305 calls, 2.18 ms/call {min521ns,Max67.17ms}) +=> Time.Benchmark 677.71 ms ( 1 call, 677.71 ms/call {min677.71ms,Max677.71ms}) + => Time.Alignment 677.21 ms ( 99.93 %) ( 305 calls, 2.22 ms/call {min546ns,Max65.83ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.p2.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --affine-penalties=0,5,3,2" - User time (seconds): 0.66 + User time (seconds): 0.67 System time (seconds): 0.00 - Percent of CPU this job got: 100% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.66 + Percent of CPU this job got: 99% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.67 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 4944 + Maximum resident set size (kbytes): 4976 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 677 + Minor (reclaiming a frame) page faults: 676 Voluntary context switches: 1 Involuntary context switches: 3 Swaps: 0 @@ -1845,23 +1845,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 833.40 ms ( 1 call, 833.40 ms/call {min833.40ms,Max833.40ms}) - => Time.Alignment 832.64 ms ( 99.91 %) ( 305 calls, 2.73 ms/call {min519ns,Max76.62ms}) +=> Time.Benchmark 799.91 ms ( 1 call, 799.91 ms/call {min799.91ms,Max799.91ms}) + => Time.Alignment 799.31 ms ( 99.92 %) ( 305 calls, 2.62 ms/call {min512ns,Max74.60ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.p3.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --affine-penalties=-5,1,2,1" - User time (seconds): 0.83 + User time (seconds): 0.80 System time (seconds): 0.00 Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.83 + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.80 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 5344 + Maximum resident set size (kbytes): 5352 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 841 Voluntary context switches: 1 - Involuntary context switches: 3 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1872,8 +1872,8 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 385.57 ms ( 1 call, 385.57 ms/call {min385.57ms,Max385.57ms}) - => Time.Alignment 385.14 ms ( 99.89 %) ( 305 calls, 1.26 ms/call {min503ns,Max36.70ms}) +=> Time.Benchmark 383.13 ms ( 1 call, 383.13 ms/call {min383.13ms,Max383.13ms}) + => Time.Alignment 382.61 ms ( 99.86 %) ( 305 calls, 1.25 ms/call {min514ns,Max35.61ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.p4.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --affine-penalties=-2,3,1,4" User time (seconds): 0.38 System time (seconds): 0.00 @@ -1888,7 +1888,7 @@ Major (requiring I/O) page faults: 0 Minor (reclaiming a frame) page faults: 396 Voluntary context switches: 1 - Involuntary context switches: 0 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1899,23 +1899,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 1.24 s ( 1 call, 1.24 s/call {min1.24s,Max1.24s}) - => Time.Alignment 1.24 s ( 99.94 %) ( 305 calls, 4.07 ms/call {min516ns,Max113.42ms}) +=> Time.Benchmark 1.18 s ( 1 call, 1.18 s/call {min1.18s,Max1.18s}) + => Time.Alignment 1.18 s ( 99.95 %) ( 305 calls, 3.86 ms/call {min533ns,Max109.37ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.p5.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --affine-penalties=-3,5,3,2" - User time (seconds): 1.23 + User time (seconds): 1.17 System time (seconds): 0.00 - Percent of CPU this job got: 99% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.24 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:01.17 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 6136 + Maximum resident set size (kbytes): 6124 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 1037 + Minor (reclaiming a frame) page faults: 1033 Voluntary context switches: 1 - Involuntary context switches: 10 + Involuntary context switches: 4 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1926,23 +1926,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 78.84 ms ( 1 call, 78.84 ms/call {min78.84ms,Max78.84ms}) - => Time.Alignment 78.27 ms ( 99.28 %) ( 305 calls, 256.63 us/call {min512ns,Max9.48ms}) +=> Time.Benchmark 121.53 ms ( 1 call, 121.53 ms/call {min121.53ms,Max121.53ms}) + => Time.Alignment 120.15 ms ( 98.87 %) ( 305 calls, 393.93 us/call {min515ns,Max16.39ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.wfapt0.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1" - User time (seconds): 0.07 + User time (seconds): 0.11 System time (seconds): 0.00 - Percent of CPU this job got: 97% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.07 + Percent of CPU this job got: 98% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.12 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 2884 + Maximum resident set size (kbytes): 2936 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 199 + Minor (reclaiming a frame) page faults: 198 Voluntary context switches: 1 - Involuntary context switches: 2 + Involuntary context switches: 3 Swaps: 0 File system inputs: 0 File system outputs: 8 @@ -1953,23 +1953,23 @@ Exit status: 0 [Benchmark] => Total.reads 305 -=> Time.Benchmark 460.09 ms ( 1 call, 460.09 ms/call {min460.09ms,Max460.09ms}) - => Time.Alignment 458.98 ms ( 99.76 %) ( 305 calls, 1.50 ms/call {min509ns,Max51.17ms}) +=> Time.Benchmark 380.88 ms ( 1 call, 380.88 ms/call {min380.88ms,Max380.88ms}) + => Time.Alignment 380.46 ms ( 99.89 %) ( 305 calls, 1.25 ms/call {min507ns,Max38.74ms}) Command being timed: "./bin/align_benchmark -i ./tests/wfa.utest.seq -o ./tests/test.biwfa.score.affine.wfapt1.alg -a gap-affine-wfa --wfa-memory-mode=ultralow --wfa-score-only --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10" - User time (seconds): 0.44 + User time (seconds): 0.38 System time (seconds): 0.00 - Percent of CPU this job got: 98% - Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.46 + Percent of CPU this job got: 100% + Elapsed (wall clock) time (h:mm:ss or m:ss): 0:00.38 Average shared text size (kbytes): 0 Average unshared data size (kbytes): 0 Average stack size (kbytes): 0 Average total size (kbytes): 0 - Maximum resident set size (kbytes): 3828 + Maximum resident set size (kbytes): 3868 Average resident set size (kbytes): 0 Major (requiring I/O) page faults: 0 - Minor (reclaiming a frame) page faults: 461 + Minor (reclaiming a frame) page faults: 460 Voluntary context switches: 1 - Involuntary context switches: 10 + Involuntary context switches: 1 Swaps: 0 File system inputs: 0 File system outputs: 8 diff --git a/wavefront/wavefront_aligner.c b/wavefront/wavefront_aligner.c index ee4dd3e..14cca9c 100644 --- a/wavefront/wavefront_aligner.c +++ b/wavefront/wavefront_aligner.c @@ -94,23 +94,23 @@ void wavefront_aligner_init_penalties( wavefront_aligner_attr_t* const attributes) { switch (attributes->distance_metric) { case indel: - wavefronts_penalties_set_indel(&wf_aligner->penalties); + wavefront_penalties_set_indel(&wf_aligner->penalties); break; case edit: - wavefronts_penalties_set_edit(&wf_aligner->penalties); + wavefront_penalties_set_edit(&wf_aligner->penalties); break; case gap_linear: - wavefronts_penalties_set_linear( + wavefront_penalties_set_linear( &wf_aligner->penalties, &attributes->linear_penalties); break; case gap_affine: - wavefronts_penalties_set_affine( + wavefront_penalties_set_affine( &wf_aligner->penalties, &attributes->affine_penalties); break; case gap_affine_2p: - wavefronts_penalties_set_affine2p( + wavefront_penalties_set_affine2p( &wf_aligner->penalties, &attributes->affine2p_penalties); break; diff --git a/wavefront/wavefront_aligner.h b/wavefront/wavefront_aligner.h index 2296b0c..fcc9bda 100644 --- a/wavefront/wavefront_aligner.h +++ b/wavefront/wavefront_aligner.h @@ -104,7 +104,7 @@ typedef struct _wavefront_aligner_t { // Alignment Attributes alignment_scope_t alignment_scope; // Alignment scope (score only or full-CIGAR) alignment_form_t alignment_form; // Alignment form (end-to-end/ends-free) - wavefronts_penalties_t penalties; // Alignment penalties + wavefront_penalties_t penalties; // Alignment penalties wavefront_heuristic_t heuristic; // Heuristic's parameters wavefront_memory_t memory_mode; // Wavefront memory strategy (modular wavefronts and piggyback) // Wavefront components diff --git a/wavefront/wavefront_backtrace.c b/wavefront/wavefront_backtrace.c index 04a75cd..c41b9a9 100644 --- a/wavefront/wavefront_backtrace.c +++ b/wavefront/wavefront_backtrace.c @@ -60,7 +60,7 @@ typedef enum { /* * Backtrace Trace Patch Match/Mismsmatch */ -int64_t wavefronts_backtrace_misms( +int64_t wavefront_backtrace_misms( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -74,7 +74,7 @@ int64_t wavefronts_backtrace_misms( return WAVEFRONT_OFFSET_NULL; } } -void wavefronts_backtrace_matches( +void wavefront_backtrace_matches( wavefront_aligner_t* const wf_aligner, const int k, wf_offset_t offset, @@ -101,7 +101,7 @@ void wavefronts_backtrace_matches( /* * Backtrace Trace Patch Deletion */ -int64_t wavefronts_backtrace_del1_open( +int64_t wavefront_backtrace_del1_open( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -115,7 +115,7 @@ int64_t wavefronts_backtrace_del1_open( return WAVEFRONT_OFFSET_NULL; } } -int64_t wavefronts_backtrace_del2_open( +int64_t wavefront_backtrace_del2_open( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -129,7 +129,7 @@ int64_t wavefronts_backtrace_del2_open( return WAVEFRONT_OFFSET_NULL; } } -int64_t wavefronts_backtrace_del1_ext( +int64_t wavefront_backtrace_del1_ext( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -143,7 +143,7 @@ int64_t wavefronts_backtrace_del1_ext( return WAVEFRONT_OFFSET_NULL; } } -int64_t wavefronts_backtrace_del2_ext( +int64_t wavefront_backtrace_del2_ext( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -160,7 +160,7 @@ int64_t wavefronts_backtrace_del2_ext( /* * Backtrace Trace Patch Insertion */ -int64_t wavefronts_backtrace_ins1_open( +int64_t wavefront_backtrace_ins1_open( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -174,7 +174,7 @@ int64_t wavefronts_backtrace_ins1_open( return WAVEFRONT_OFFSET_NULL; } } -int64_t wavefronts_backtrace_ins2_open( +int64_t wavefront_backtrace_ins2_open( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -188,7 +188,7 @@ int64_t wavefronts_backtrace_ins2_open( return WAVEFRONT_OFFSET_NULL; } } -int64_t wavefronts_backtrace_ins1_ext( +int64_t wavefront_backtrace_ins1_ext( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -202,7 +202,7 @@ int64_t wavefronts_backtrace_ins1_ext( return WAVEFRONT_OFFSET_NULL; } } -int64_t wavefronts_backtrace_ins2_ext( +int64_t wavefront_backtrace_ins2_ext( wavefront_aligner_t* const wf_aligner, const int score, const int k) { @@ -228,7 +228,7 @@ void wavefront_backtrace_linear( const int pattern_length = wf_aligner->pattern_length; const int text_length = wf_aligner->text_length; const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric; - const wavefronts_penalties_t* const wavefront_penalties = &(wf_aligner->penalties); + const wavefront_penalties_t* const wavefront_penalties = &(wf_aligner->penalties); // Prepare cigar cigar_t* const cigar = wf_aligner->cigar; cigar->end_offset = cigar->max_operations - 1; @@ -256,15 +256,15 @@ void wavefront_backtrace_linear( const int gap_open1 = score - wavefront_penalties->gap_opening1; // Compute source offsets const int64_t misms = (distance_metric != indel) ? - wavefronts_backtrace_misms(wf_aligner,mismatch,k) : + wavefront_backtrace_misms(wf_aligner,mismatch,k) : WAVEFRONT_OFFSET_NULL; - const int64_t ins = wavefronts_backtrace_ins1_open(wf_aligner,gap_open1,k); - const int64_t del = wavefronts_backtrace_del1_open(wf_aligner,gap_open1,k); + const int64_t ins = wavefront_backtrace_ins1_open(wf_aligner,gap_open1,k); + const int64_t del = wavefront_backtrace_del1_open(wf_aligner,gap_open1,k); const int64_t max_all = MAX(misms,MAX(ins,del)); // Traceback Matches const int max_offset = BACKTRACE_PIGGYBACK_GET_OFFSET(max_all); const int num_matches = offset - max_offset; - wavefronts_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); + wavefront_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); offset = max_offset; // Update coordinates v = WAVEFRONT_V(k,offset); @@ -301,7 +301,7 @@ void wavefront_backtrace_linear( if (v > 0 && h > 0) { // score == 0 // Account for beginning series of matches const int num_matches = MIN(v,h); - wavefronts_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); + wavefront_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); v -= num_matches; h -= num_matches; } @@ -323,7 +323,7 @@ void wavefront_backtrace_affine( const int pattern_length = wf_aligner->pattern_length; const int text_length = wf_aligner->text_length; const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric; - const wavefronts_penalties_t* const wavefront_penalties = &(wf_aligner->penalties); + const wavefront_penalties_t* const wavefront_penalties = &(wf_aligner->penalties); // Prepare cigar cigar_t* const cigar = wf_aligner->cigar; cigar->end_offset = cigar->max_operations - 1; @@ -359,21 +359,21 @@ void wavefront_backtrace_affine( int64_t max_all; switch (matrix_type) { case affine2p_matrix_M: { - const int64_t misms = wavefronts_backtrace_misms(wf_aligner,mismatch,k); - const int64_t ins1_open = wavefronts_backtrace_ins1_open(wf_aligner,gap_open1,k); - const int64_t ins1_ext = wavefronts_backtrace_ins1_ext(wf_aligner,gap_extend1,k); + const int64_t misms = wavefront_backtrace_misms(wf_aligner,mismatch,k); + const int64_t ins1_open = wavefront_backtrace_ins1_open(wf_aligner,gap_open1,k); + const int64_t ins1_ext = wavefront_backtrace_ins1_ext(wf_aligner,gap_extend1,k); const int64_t max_ins1 = MAX(ins1_open,ins1_ext); - const int64_t del1_open = wavefronts_backtrace_del1_open(wf_aligner,gap_open1,k); - const int64_t del1_ext = wavefronts_backtrace_del1_ext(wf_aligner,gap_extend1,k); + const int64_t del1_open = wavefront_backtrace_del1_open(wf_aligner,gap_open1,k); + const int64_t del1_ext = wavefront_backtrace_del1_ext(wf_aligner,gap_extend1,k); const int64_t max_del1 = MAX(del1_open,del1_ext); if (distance_metric == gap_affine) { max_all = MAX(misms,MAX(max_ins1,max_del1)); break; } - const int64_t ins2_open = wavefronts_backtrace_ins2_open(wf_aligner,gap_open2,k); - const int64_t ins2_ext = wavefronts_backtrace_ins2_ext(wf_aligner,gap_extend2,k); + const int64_t ins2_open = wavefront_backtrace_ins2_open(wf_aligner,gap_open2,k); + const int64_t ins2_ext = wavefront_backtrace_ins2_ext(wf_aligner,gap_extend2,k); const int64_t max_ins2 = MAX(ins2_open,ins2_ext); - const int64_t del2_open = wavefronts_backtrace_del2_open(wf_aligner,gap_open2,k); - const int64_t del2_ext = wavefronts_backtrace_del2_ext(wf_aligner,gap_extend2,k); + const int64_t del2_open = wavefront_backtrace_del2_open(wf_aligner,gap_open2,k); + const int64_t del2_ext = wavefront_backtrace_del2_ext(wf_aligner,gap_extend2,k); const int64_t max_del2 = MAX(del2_open,del2_ext); const int64_t max_ins = MAX(max_ins1,max_ins2); const int64_t max_del = MAX(max_del1,max_del2); @@ -381,26 +381,26 @@ void wavefront_backtrace_affine( break; } case affine2p_matrix_I1: { - const int64_t ins1_open = wavefronts_backtrace_ins1_open(wf_aligner,gap_open1,k); - const int64_t ins1_ext = wavefronts_backtrace_ins1_ext(wf_aligner,gap_extend1,k); + const int64_t ins1_open = wavefront_backtrace_ins1_open(wf_aligner,gap_open1,k); + const int64_t ins1_ext = wavefront_backtrace_ins1_ext(wf_aligner,gap_extend1,k); max_all = MAX(ins1_open,ins1_ext); break; } case affine2p_matrix_I2: { - const int64_t ins2_open = wavefronts_backtrace_ins2_open(wf_aligner,gap_open2,k); - const int64_t ins2_ext = wavefronts_backtrace_ins2_ext(wf_aligner,gap_extend2,k); + const int64_t ins2_open = wavefront_backtrace_ins2_open(wf_aligner,gap_open2,k); + const int64_t ins2_ext = wavefront_backtrace_ins2_ext(wf_aligner,gap_extend2,k); max_all = MAX(ins2_open,ins2_ext); break; } case affine2p_matrix_D1: { - const int64_t del1_open = wavefronts_backtrace_del1_open(wf_aligner,gap_open1,k); - const int64_t del1_ext = wavefronts_backtrace_del1_ext(wf_aligner,gap_extend1,k); + const int64_t del1_open = wavefront_backtrace_del1_open(wf_aligner,gap_open1,k); + const int64_t del1_ext = wavefront_backtrace_del1_ext(wf_aligner,gap_extend1,k); max_all = MAX(del1_open,del1_ext); break; } case affine2p_matrix_D2: { - const int64_t del2_open = wavefronts_backtrace_del2_open(wf_aligner,gap_open2,k); - const int64_t del2_ext = wavefronts_backtrace_del2_ext(wf_aligner,gap_extend2,k); + const int64_t del2_open = wavefront_backtrace_del2_open(wf_aligner,gap_open2,k); + const int64_t del2_ext = wavefront_backtrace_del2_ext(wf_aligner,gap_extend2,k); max_all = MAX(del2_open,del2_ext); break; } @@ -413,7 +413,7 @@ void wavefront_backtrace_affine( if (matrix_type == affine2p_matrix_M) { const int max_offset = BACKTRACE_PIGGYBACK_GET_OFFSET(max_all); const int num_matches = offset - max_offset; - wavefronts_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); + wavefront_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); offset = max_offset; // Update coordinates v = WAVEFRONT_V(k,offset); @@ -497,7 +497,7 @@ void wavefront_backtrace_affine( if (v > 0 && h > 0) { // score == 0 // Account for beginning series of matches const int num_matches = MIN(v,h); - wavefronts_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); + wavefront_backtrace_matches(wf_aligner,k,offset,num_matches,cigar); v -= num_matches; h -= num_matches; } diff --git a/wavefront/wavefront_components.c b/wavefront/wavefront_components.c index 278eebf..50213a9 100644 --- a/wavefront/wavefront_components.c +++ b/wavefront/wavefront_components.c @@ -60,7 +60,7 @@ void wavefront_components_dimensions_edit( } void wavefront_components_dimensions_linear( wavefront_components_t* const wf_components, - wavefronts_penalties_t* const penalties, + wavefront_penalties_t* const penalties, const int max_pattern_length, const int max_text_length, int* const max_score_scope, @@ -79,7 +79,7 @@ void wavefront_components_dimensions_linear( } void wavefront_components_dimensions_affine( wavefront_components_t* const wf_components, - wavefronts_penalties_t* const penalties, + wavefront_penalties_t* const penalties, const int max_pattern_length, const int max_text_length, int* const max_score_scope, @@ -99,7 +99,7 @@ void wavefront_components_dimensions_affine( } void wavefront_components_dimensions_affine2p( wavefront_components_t* const wf_components, - wavefronts_penalties_t* const penalties, + wavefront_penalties_t* const penalties, const int max_pattern_length, const int max_text_length, int* const max_score_scope, @@ -123,7 +123,7 @@ void wavefront_components_dimensions_affine2p( } void wavefront_components_dimensions( wavefront_components_t* const wf_components, - wavefronts_penalties_t* const penalties, + wavefront_penalties_t* const penalties, const int max_pattern_length, const int max_text_length, int* const max_score_scope, @@ -195,7 +195,7 @@ void wavefront_components_allocate( wavefront_components_t* const wf_components, const int max_pattern_length, const int max_text_length, - wavefronts_penalties_t* const penalties, + wavefront_penalties_t* const penalties, const bool memory_modular, const bool bt_piggyback, mm_allocator_t* const mm_allocator) { @@ -279,7 +279,7 @@ void wavefront_components_resize( wavefront_components_t* const wf_components, const int max_pattern_length, const int max_text_length, - wavefronts_penalties_t* const penalties) { + wavefront_penalties_t* const penalties) { // Compute dimensions int num_wavefronts = 0; wavefront_components_dimensions( diff --git a/wavefront/wavefront_components.h b/wavefront/wavefront_components.h index b6383c8..227759c 100644 --- a/wavefront/wavefront_components.h +++ b/wavefront/wavefront_components.h @@ -70,7 +70,7 @@ void wavefront_components_allocate( wavefront_components_t* const wf_components, const int max_pattern_length, const int max_text_length, - wavefronts_penalties_t* const penalties, + wavefront_penalties_t* const penalties, const bool memory_modular, const bool bt_piggyback, mm_allocator_t* const mm_allocator); @@ -88,7 +88,7 @@ void wavefront_components_resize( wavefront_components_t* const wf_components, const int max_pattern_length, const int max_text_length, - wavefronts_penalties_t* const penalties); + wavefront_penalties_t* const penalties); void wavefront_components_resize_null__victim( wavefront_components_t* const wf_components, const int lo, diff --git a/wavefront/wavefront_compute.c b/wavefront/wavefront_compute.c index 6ac4713..152631d 100644 --- a/wavefront/wavefront_compute.c +++ b/wavefront/wavefront_compute.c @@ -133,7 +133,7 @@ void wavefront_compute_fetch_input( wavefront_components_t* const wf_components = &wf_aligner->wf_components; const distance_metric_t distance_metric = wf_aligner->penalties.distance_metric; // Compute scores - const wavefronts_penalties_t* const penalties = &(wf_aligner->penalties); + const wavefront_penalties_t* const penalties = &(wf_aligner->penalties); if (distance_metric == gap_linear) { int mismatch = score - penalties->mismatch; int gap_open1 = score - penalties->gap_opening1; diff --git a/wavefront/wavefront_debug.c b/wavefront/wavefront_debug.c index 4c896f4..673322b 100644 --- a/wavefront/wavefront_debug.c +++ b/wavefront/wavefront_debug.c @@ -144,7 +144,7 @@ void wavefront_report_lite( fprintf(stream,","); wavefront_aligner_print_scope(stream,wf_aligner); fprintf(stream,","); - wavefronts_penalties_print(stream,&wf_aligner->penalties); + wavefront_penalties_print(stream,&wf_aligner->penalties); fprintf(stream,"]\t"); cigar_print(stream,wf_aligner->cigar,true); if (wf_aligner->match_funct != NULL) { @@ -179,7 +179,7 @@ void wavefront_report_verbose_begin( wf_aligner->system.max_alignment_score); // Penalties fprintf(stream," Penalties="); - wavefronts_penalties_print(stream,&wf_aligner->penalties); + wavefront_penalties_print(stream,&wf_aligner->penalties); // Heuristic fprintf(stream," Heuristic="); wavefront_heuristic_print(stream,&wf_aligner->heuristic); diff --git a/wavefront/wavefront_heuristic.c b/wavefront/wavefront_heuristic.c index e58234f..0eb6409 100644 --- a/wavefront/wavefront_heuristic.c +++ b/wavefront/wavefront_heuristic.c @@ -412,7 +412,7 @@ void wavefront_heuristic_zdrop( wf_aligner,wavefront,score,sw_scores, &cmax_sw_score,&cmax_k,&cmax_offset); // Apply Z-Drop - wavefronts_penalties_t* const penalties = &wf_aligner->penalties; + wavefront_penalties_t* const penalties = &wf_aligner->penalties; const int gap_e = (penalties->gap_extension1 > 0) ? penalties->gap_extension1 : 1; const int zdrop = wf_heuristic->zdrop; const int max_sw_score = wf_heuristic->max_sw_score; diff --git a/wavefront/wavefront_penalties.c b/wavefront/wavefront_penalties.c index 4f6739e..c76a37d 100644 --- a/wavefront/wavefront_penalties.c +++ b/wavefront/wavefront_penalties.c @@ -34,33 +34,33 @@ /* * Penalties adjustment */ -void wavefronts_penalties_set_indel( - wavefronts_penalties_t* const wavefronts_penalties) { +void wavefront_penalties_set_indel( + wavefront_penalties_t* const wf_penalties) { // Set distance model - wavefronts_penalties->distance_metric = indel; + wf_penalties->distance_metric = indel; // Set penalties - wavefronts_penalties->mismatch = -1; - wavefronts_penalties->gap_opening1 = 1; - wavefronts_penalties->gap_extension1 = -1; - wavefronts_penalties->gap_opening2 = -1; - wavefronts_penalties->gap_extension2 = -1; + wf_penalties->mismatch = -1; + wf_penalties->gap_opening1 = 1; + wf_penalties->gap_extension1 = -1; + wf_penalties->gap_opening2 = -1; + wf_penalties->gap_extension2 = -1; } -void wavefronts_penalties_set_edit( - wavefronts_penalties_t* const wavefronts_penalties) { +void wavefront_penalties_set_edit( + wavefront_penalties_t* const wf_penalties) { // Set distance model - wavefronts_penalties->distance_metric = edit; + wf_penalties->distance_metric = edit; // Set penalties - wavefronts_penalties->mismatch = 1; - wavefronts_penalties->gap_opening1 = 1; - wavefronts_penalties->gap_extension1 = -1; - wavefronts_penalties->gap_opening2 = -1; - wavefronts_penalties->gap_extension2 = -1; + wf_penalties->mismatch = 1; + wf_penalties->gap_opening1 = 1; + wf_penalties->gap_extension1 = -1; + wf_penalties->gap_opening2 = -1; + wf_penalties->gap_extension2 = -1; } -void wavefronts_penalties_set_linear( - wavefronts_penalties_t* const wavefronts_penalties, +void wavefront_penalties_set_linear( + wavefront_penalties_t* const wf_penalties, linear_penalties_t* const linear_penalties) { // Set distance model - wavefronts_penalties->distance_metric = gap_linear; + wf_penalties->distance_metric = gap_linear; // Check base penalties if (linear_penalties->match > 0) { fprintf(stderr,"[WFA::Penalties] Match score must be negative or zero (M=%d)\n",linear_penalties->match); @@ -72,24 +72,24 @@ void wavefronts_penalties_set_linear( } // Set penalties (if needed, adjust using Eizenga's formula) if (linear_penalties->match < 0) { - wavefronts_penalties->match = linear_penalties->match; - wavefronts_penalties->mismatch = 2*linear_penalties->mismatch - 2*linear_penalties->match; - wavefronts_penalties->gap_opening1 = 2*linear_penalties->indel - linear_penalties->match; + wf_penalties->match = linear_penalties->match; + wf_penalties->mismatch = 2*linear_penalties->mismatch - 2*linear_penalties->match; + wf_penalties->gap_opening1 = 2*linear_penalties->indel - linear_penalties->match; } else { - wavefronts_penalties->match = 0; - wavefronts_penalties->mismatch = linear_penalties->mismatch; - wavefronts_penalties->gap_opening1 = linear_penalties->indel; + wf_penalties->match = 0; + wf_penalties->mismatch = linear_penalties->mismatch; + wf_penalties->gap_opening1 = linear_penalties->indel; } // Set unused - wavefronts_penalties->gap_extension1 = -1; - wavefronts_penalties->gap_opening2 = -1; - wavefronts_penalties->gap_extension2 = -1; + wf_penalties->gap_extension1 = -1; + wf_penalties->gap_opening2 = -1; + wf_penalties->gap_extension2 = -1; } -void wavefronts_penalties_set_affine( - wavefronts_penalties_t* const wavefronts_penalties, +void wavefront_penalties_set_affine( + wavefront_penalties_t* const wf_penalties, affine_penalties_t* const affine_penalties) { // Set distance model - wavefronts_penalties->distance_metric = gap_affine; + wf_penalties->distance_metric = gap_affine; // Check base penalties if (affine_penalties->match > 0) { fprintf(stderr,"[WFA::Penalties] Match score must be negative or zero (M=%d)\n",affine_penalties->match); @@ -105,25 +105,25 @@ void wavefronts_penalties_set_affine( } // Set penalties (if needed, adjust using Eizenga's formula) if (affine_penalties->match < 0) { - wavefronts_penalties->match = affine_penalties->match; - wavefronts_penalties->mismatch = 2*affine_penalties->mismatch - 2*affine_penalties->match; - wavefronts_penalties->gap_opening1 = 2*affine_penalties->gap_opening; - wavefronts_penalties->gap_extension1 = 2*affine_penalties->gap_extension - affine_penalties->match; + wf_penalties->match = affine_penalties->match; + wf_penalties->mismatch = 2*affine_penalties->mismatch - 2*affine_penalties->match; + wf_penalties->gap_opening1 = 2*affine_penalties->gap_opening; + wf_penalties->gap_extension1 = 2*affine_penalties->gap_extension - affine_penalties->match; } else { - wavefronts_penalties->match = 0; - wavefronts_penalties->mismatch = affine_penalties->mismatch; - wavefronts_penalties->gap_opening1 = affine_penalties->gap_opening; - wavefronts_penalties->gap_extension1 = affine_penalties->gap_extension; + wf_penalties->match = 0; + wf_penalties->mismatch = affine_penalties->mismatch; + wf_penalties->gap_opening1 = affine_penalties->gap_opening; + wf_penalties->gap_extension1 = affine_penalties->gap_extension; } // Set unused - wavefronts_penalties->gap_opening2 = -1; - wavefronts_penalties->gap_extension2 = -1; + wf_penalties->gap_opening2 = -1; + wf_penalties->gap_extension2 = -1; } -void wavefronts_penalties_set_affine2p( - wavefronts_penalties_t* const wavefronts_penalties, +void wavefront_penalties_set_affine2p( + wavefront_penalties_t* const wf_penalties, affine2p_penalties_t* const affine2p_penalties) { // Set distance model - wavefronts_penalties->distance_metric = gap_affine_2p; + wf_penalties->distance_metric = gap_affine_2p; // Check base penalties if (affine2p_penalties->match > 0) { fprintf(stderr,"[WFA::Penalties] Match score must be negative or zero (M=%d)\n",affine2p_penalties->match); @@ -143,29 +143,29 @@ void wavefronts_penalties_set_affine2p( } // Set penalties (if needed, adjust using Eizenga's formula) if (affine2p_penalties->match < 0) { - wavefronts_penalties->match = affine2p_penalties->match; - wavefronts_penalties->mismatch = 2*affine2p_penalties->mismatch - 2*wavefronts_penalties->match; - wavefronts_penalties->gap_opening1 = 2*affine2p_penalties->gap_opening1; - wavefronts_penalties->gap_extension1 = 2*affine2p_penalties->gap_extension1 - affine2p_penalties->match; - wavefronts_penalties->gap_opening2 = 2*affine2p_penalties->gap_opening2; - wavefronts_penalties->gap_extension2 = 2*affine2p_penalties->gap_extension2 - affine2p_penalties->match; + wf_penalties->match = affine2p_penalties->match; + wf_penalties->mismatch = 2*affine2p_penalties->mismatch - 2*wf_penalties->match; + wf_penalties->gap_opening1 = 2*affine2p_penalties->gap_opening1; + wf_penalties->gap_extension1 = 2*affine2p_penalties->gap_extension1 - affine2p_penalties->match; + wf_penalties->gap_opening2 = 2*affine2p_penalties->gap_opening2; + wf_penalties->gap_extension2 = 2*affine2p_penalties->gap_extension2 - affine2p_penalties->match; } else { - wavefronts_penalties->match = 0; - wavefronts_penalties->mismatch = affine2p_penalties->mismatch; - wavefronts_penalties->gap_opening1 = affine2p_penalties->gap_opening1; - wavefronts_penalties->gap_extension1 = affine2p_penalties->gap_extension1; - wavefronts_penalties->gap_opening2 = affine2p_penalties->gap_opening2; - wavefronts_penalties->gap_extension2 = affine2p_penalties->gap_extension2; + wf_penalties->match = 0; + wf_penalties->mismatch = affine2p_penalties->mismatch; + wf_penalties->gap_opening1 = affine2p_penalties->gap_opening1; + wf_penalties->gap_extension1 = affine2p_penalties->gap_extension1; + wf_penalties->gap_opening2 = affine2p_penalties->gap_opening2; + wf_penalties->gap_extension2 = affine2p_penalties->gap_extension2; } } /* * Display */ -void wavefronts_penalties_print( +void wavefront_penalties_print( FILE* const stream, - wavefronts_penalties_t* const wavefronts_penalties) { + wavefront_penalties_t* const wf_penalties) { // Select penalties mode - switch (wavefronts_penalties->distance_metric) { + switch (wf_penalties->distance_metric) { case indel: fprintf(stream,"(Indel)"); break; @@ -174,22 +174,22 @@ void wavefronts_penalties_print( break; case gap_linear: fprintf(stream,"(GapLinear,%d,%d)", - wavefronts_penalties->mismatch, - wavefronts_penalties->gap_opening1); + wf_penalties->mismatch, + wf_penalties->gap_opening1); break; case gap_affine: fprintf(stream,"(GapAffine,%d,%d,%d)", - wavefronts_penalties->mismatch, - wavefronts_penalties->gap_opening1, - wavefronts_penalties->gap_extension1); + wf_penalties->mismatch, + wf_penalties->gap_opening1, + wf_penalties->gap_extension1); break; case gap_affine_2p: fprintf(stream,"(GapAffine2p,%d,%d,%d,%d,%d)", - wavefronts_penalties->mismatch, - wavefronts_penalties->gap_opening1, - wavefronts_penalties->gap_extension1, - wavefronts_penalties->gap_opening2, - wavefronts_penalties->gap_extension2); + wf_penalties->mismatch, + wf_penalties->gap_opening1, + wf_penalties->gap_extension1, + wf_penalties->gap_opening2, + wf_penalties->gap_extension2); break; default: break; diff --git a/wavefront/wavefront_penalties.h b/wavefront/wavefront_penalties.h index 37dc6dc..97c752c 100644 --- a/wavefront/wavefront_penalties.h +++ b/wavefront/wavefront_penalties.h @@ -58,7 +58,7 @@ typedef struct { int gap_extension1; // (E1 > 0) int gap_opening2; // (O2 >= 0) int gap_extension2; // (E2 > 0) -} wavefronts_penalties_t; +} wavefront_penalties_t; /* * Compute SW-score equivalent (thanks to Eizenga's formula) @@ -68,44 +68,44 @@ typedef struct { /* * Penalties adjustment */ -void wavefronts_penalties_set_indel( - wavefronts_penalties_t* const wavefronts_penalties); -void wavefronts_penalties_set_edit( - wavefronts_penalties_t* const wavefronts_penalties); -void wavefronts_penalties_set_linear( - wavefronts_penalties_t* const wavefronts_penalties, +void wavefront_penalties_set_indel( + wavefront_penalties_t* const wf_penalties); +void wavefront_penalties_set_edit( + wavefront_penalties_t* const wf_penalties); +void wavefront_penalties_set_linear( + wavefront_penalties_t* const wf_penalties, linear_penalties_t* const linear_penalties); -void wavefronts_penalties_set_affine( - wavefronts_penalties_t* const wavefronts_penalties, +void wavefront_penalties_set_affine( + wavefront_penalties_t* const wf_penalties, affine_penalties_t* const affine_penalties); -void wavefronts_penalties_set_affine2p( - wavefronts_penalties_t* const wavefronts_penalties, +void wavefront_penalties_set_affine2p( + wavefront_penalties_t* const wf_penalties, affine2p_penalties_t* const affine2p_penalties); /* * Score conversion */ -int wavefronts_penalties_get_score_indel( - wavefronts_penalties_t* const wavefronts_penalties, +int wavefront_penalties_get_score_indel( + wavefront_penalties_t* const wf_penalties, const int score); -int wavefronts_penalties_get_score_edit( - wavefronts_penalties_t* const wavefronts_penalties, +int wavefront_penalties_get_score_edit( + wavefront_penalties_t* const wf_penalties, const int score); -int wavefronts_penalties_get_score_linear( - wavefronts_penalties_t* const wavefronts_penalties, +int wavefront_penalties_get_score_linear( + wavefront_penalties_t* const wf_penalties, const int score); -int wavefronts_penalties_get_score_affine( - wavefronts_penalties_t* const wavefronts_penalties, +int wavefront_penalties_get_score_affine( + wavefront_penalties_t* const wf_penalties, const int score); -int wavefronts_penalties_get_score_affine2p( - wavefronts_penalties_t* const wavefronts_penalties, +int wavefront_penalties_get_score_affine2p( + wavefront_penalties_t* const wf_penalties, const int score); /* * Display */ -void wavefronts_penalties_print( +void wavefront_penalties_print( FILE* const stream, - wavefronts_penalties_t* const wavefronts_penalties); + wavefront_penalties_t* const wf_penalties); #endif /* WAVEFRONT_WAVEFRONT_PENALTIES_H_ */ diff --git a/wavefront/wavefront_plot.c b/wavefront/wavefront_plot.c index 4d03644..dfd96b0 100644 --- a/wavefront/wavefront_plot.c +++ b/wavefront/wavefront_plot.c @@ -206,7 +206,7 @@ void wavefront_plot_print( fprintf(stream,"# PatternLength %d\n",wf_aligner->pattern_length); fprintf(stream,"# TextLength %d\n",wf_aligner->text_length); fprintf(stream,"# Penalties "); - wavefronts_penalties_print(stream,&wf_aligner->penalties); + wavefront_penalties_print(stream,&wf_aligner->penalties); fprintf(stream,"\n"); // Alignment mode fprintf(stream,"# WFAMode (");