Merge pull request #371 from vgteam/no-gam-chunk

Add a no-GAM chunk to the Cactus example

README.md

@@ -145,8 +145,8 @@ For example:
 
 ```
 cd exampleData/
-../scripts/prepare_chunk.sh -x mygraph.xg -h mygraph.gbwt -r chr1:1-100 -d 'Region A' -o chunk-chr1-1-100 -g mygam1.gam -g mygam2.gam >> mychunks.bed
-../scripts/prepare_chunk.sh -x mygraph.xg -h mygraph.gbwt -r chr1:101-200 -d 'Region B' -o chunk-chr1-100-200 -g mygam1.gam -g mygam2.gam >> mychunks.bed
+../scripts/prepare_chunks.sh -x mygraph.xg -h mygraph.gbwt -r chr1:1-100 -d 'Region A' -o chunk-chr1-1-100 -g mygam1.gam -g mygam2.gam >> mychunks.bed
+../scripts/prepare_chunks.sh -x mygraph.xg -h mygraph.gbwt -r chr1:101-200 -d 'Region B' -o chunk-chr1-100-200 -g mygam1.gam -g mygam2.gam >> mychunks.bed
 ```
 
 The BED file linking to the chunks has two additional nonstandard columns: 
@@ -168,7 +168,7 @@ You can use `prepare_chunks.sh` script to generate this additional `nodeColors.t
 
 ```
 cd exampleData/
-../scripts/prepare_chunk.sh -x mygraph.xg -h mygraph.gbwt -r chr1:1-100 -d 'Region A' -o chunk-chr1-1-100 -g mygam1.gam -g mygam2.gam -n "1 2 3" >> mychunks.bed
+../scripts/prepare_chunks.sh -x mygraph.xg -h mygraph.gbwt -r chr1:1-100 -d 'Region A' -o chunk-chr1-1-100 -g mygam1.gam -g mygam2.gam -n "1 2 3" >> mychunks.bed
 ```
 
 Adding this additional `n` flag will allow a string space delimited input of node names which will be outputted to `nodeColors.tsv`.

exampleData/cactus.bed

@@ -1,4 +1,5 @@
 ref	10	100	this is a test region
 ref	1000	2000	another region with a very long description to see how it will be displayed
-ref	2000	3000	pre-fecthed region	chunk-ref-2000-3000
-ref	4000	4500	pre-fecthed region but the chunk is missing	test_prechunk_missing
+ref	2000	3000	pre-fetched region	chunk-ref-2000-3000
+ref	4000	4500	pre-fetched region but the chunk is missing	test_prechunk_missing
+ref	482	2450	region without read tracks	chunk-cactus-no-reads

exampleData/chunk-cactus-no-reads/chunk.vg

@@ -0,0 +1,128 @@
+VG�
+d
+`TTTAGAAATCTCTTCTAGTTTCATTTTCCTTTTTTTTTTTTTTTTTTTGAGCCACAGTCTCACTGTCACCCAGGCTGGAGTGCCGTGGTATGATCT
+d
+`TGGCTCACTGCAACCTCCACCTCCCGGGCTGAAGTGATTCTCCTGCCTTAGCCACCTGAGTAGCTGGGATTACAGGTGTCCACCACCATGACCGGC
+d
+`TAATTTCTGTATTTTTAGTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTTTCGAACTCCTGACCTCCAGTGATCTGCCCACCTTGGCCTCCC	
+d
+`AAAGTGCTGGGATTACAGGCGTGAGCCACCATGCCCAGGTTTCAAGTTTCCTTTTCATTTCTAATACCTGCCTCAGAATTTCCTCCCCAATGTTCC
+
+d
+`ACTCCAACATTTGAGAACTGCCCAAGGACTATTCTGACTTTAAGTCACATAATCGATCCCAAGCACTCTCCTTCCATTGAAGGGTCTGACTCTCTG
+d
+`CCTTTGTGAACACAGGGTTTTAGAGAAGTAAACTTAGGGAAACCAGCTATTCTCTTGAGGCCAAGCCACTCTGTGCTTCCAGCCCTAAGCCAACAA
+d
+`CAGCCTGAATAGAAAGAATAGGGCTGATAAATAATGAATCAGCATCTTGCTCAATTGGTGGCGTTTAAATGGTTTTAAAATCTTCTCAGGTGAAAA
+d
+`ATTACCATAATTTTGTGCTCATGGCAGATTTCCAAGGGAGACTTCAAGCAGAAAATCTTTAAGGGACCCTTGCATAGCCAGAAGTCCTTTTCAGGC
+d
+`TGATGTACATAAAATATTTAGTAGCCAGGACAGTAGAAGGACTGAAGAGTGAGAGGAGCTCCCAGGGCCTGGAAAGGCCACTTTGTAAGCTCATTC
+d
+`TTGGGGTCCTGTGGCTCTGTACCTGTGGCTGGCTGCAGTCAGTAGTGGCTGTGGGGGATCTGGGGTATCAGGTAGGTGTCCAGCTCCTGGCACTGG
+d
+`TAGAGTGCTACACTGTCCAACACCCACTCTCGGGTCACCACAGGTGCCTCACACATCTGCCCAATTGCTGGAGACAGAGAACACAAGCAGAGATTA
+d
+`GTGTCAATTCATTCTCCTGGACTAGGCTCTAATCAATCGACTCCAGGGTCCTGGTTGTATGAGTTCTTAGGATTAATGAGGTAGAAGCTAATTTTT
+d
+`TTTTTTTTTTTTTGAGACGGAGTCTTGCTCTGTCGCCGAGGCTAGAGTGTGATGGCGCAATCTCGGCTCATTCAACCTCCGCCTCCTGGGTTCAAG
+d
+`CAATTCTCCTGTCTCTGCCTCCTGAGTAGCTGGAATTACAGGCACATGCCATCACACCCAGCTAATTTTTGTATTTTTAGTAGAGACGGGGGTTTC
+d
+`ACAATGTTGGCCAGGCTGCTCTGGAACTCCTGACCTCAGGTGATCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCA
+
+CCTGG
+
+CCTTTTTTTTTTTTTTTTTTTTTTTTTG
+
+NNNNN
+g
+cAGACGGAGTCTTGCTCTTGTTGCTCAGCCTGGAATGCAATGGCACGATCTCAGCTCACTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTCCTGCCTC
+
+NNNNN
+g
+cAGCCTCCCAAGTAGCAGGGATTACAGGTGCCTGCCACCATGCCAGGCTAATTGTTTTTTCTTTTTTTTCAGATGGAGTCTCACTCTGTCACTCAGGCTG
+g
+cGATTGTGATGGTGTGATCTCAGCTCACTGCAACCTCAACATCCTGGGTTCAAGCGATTCTCCTGCCTCAGTCTCCCAAGTAGCTGGGACTACAAGTGCG
+g
+cTGCCACCATGCCTGGCTAATTTTTTTTAGTATTTTTAGTAGAGATGGGGTTTCGCCATATTGGCCAGGCTGGTCTCAAACTCCTGATGTCAGGTGATCC
+g
+cGCCCTGAGGCTGAGGCAGGAGAATCATTTAAACCCAGGAGGCGGAGGTTGCAGTGAGCCAAGACTGGGCCACTGCACTCCAGCCTGCTAAGTGACAGAG		
+
+�
+GI262359905[78741]
+ 
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exampleData/chunk-cactus-no-reads/chunk_contents.txt

@@ -0,0 +1,4 @@
+chunk.vg
+chunk_0_ref_482_2449.annotate.txt
+regions.tsv
+tracks.json

exampleData/chunk-cactus-no-reads/regions.tsv

@@ -0,0 +1 @@
+ref	482	2450	chunk-cactus-no-reads/chunk_0_ref_482_2449.vg	chunk-cactus-no-reads/chunk_0_ref_482_2449.annotate.txt

exampleData/chunk-cactus-no-reads/tracks.json

@@ -0,0 +1,11 @@
+[
+  {
+    "trackFile": "exampleData/cactus.vg.xg",
+    "trackType": "graph",
+    "trackColorSettings": {
+      "mainPalette": "#000000",
+      "auxPalette": "greys",
+      "colorReadsByMappingQuality": false
+    }
+  }
+]

scripts/prepare_chunks.sh

@@ -1,6 +1,5 @@
 #!/usr/bin/env bash
 set -e
-set -x
 
 function usage() {
     echo >&2 "${0}: Extract graph and read chunks for a region, producing a referencing line for a BED file on standard output"
@@ -71,8 +70,8 @@ vg_chunk_params=(-x $GRAPH_FILE -g -c 20 -p $REGION -T -b $OUTDIR/chunk -E $OUTD
 # construct track JSON for graph file
 # get path relative to directory above the scripts directory
 GRAPH_FILE_PATH=$(realpath --relative-to $(dirname ${BASH_SOURCE[0]})/../ $GRAPH_FILE)
-echo ${GRAPH_FILE_PATH}
-GRAPH_PALETTE="$(cat " $(dirname ${BASH_SOURCE[0]})/../src/config.json" | jq '.defaultGraphColorPalette')"
+echo >&2 "Graph file: ${GRAPH_FILE_PATH}"
+GRAPH_PALETTE="$(cat "$(dirname ${BASH_SOURCE[0]})/../src/config.json" | jq '.defaultGraphColorPalette')"
 jq -n --arg trackFile "${GRAPH_FILE_PATH}" --arg trackType "graph" --argjson trackColorSettings "$GRAPH_PALETTE" '$ARGS.named' >> $OUTDIR/temp.json
 
 # construct track JSON for haplotype file, if provided