Pull request #161: Ensure one newline between CLI help footer and RUO…

… disclaimer Merge in SAT/pbmm2 from bugfix/TAK-1545-unsmoosh-license to develop * commit 'e920454fb3f3d1d0ba958d798a2bb0527259ffc4': Ensure one newline between CLI help footer and RUO disclaimer
PacificBiosciences · Jun 2, 2021 · 4e5ebb6 · 4e5ebb6
2 parents 2a62858 + e920454
commit 4e5ebb6
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Showing 3 changed files with 3 additions and 6 deletions.
diff --git a/src/AlignSettings.cpp b/src/AlignSettings.cpp
@@ -731,8 +731,7 @@ PacBio::CLI_v2::Interface AlignSettings::CreateCLI()
     SUBREAD     : -k 19 -w 10    -o 5 -O 56 -e 4 -E 1 -A 2 -B 5 -z 400 -Z 50  -r 2000   -L 0.5 -g 5000
     CCS or HiFi : -k 19 -w 10 -u -o 5 -O 56 -e 4 -E 1 -A 2 -B 5 -z 400 -Z 50  -r 2000   -L 0.5 -g 5000
     ISOSEQ      : -k 15 -w 5  -u -o 2 -O 32 -e 1 -E 0 -A 1 -B 2 -z 200 -Z 100 -r 200000 -L 0.5 -g 2000 -C 5 -G 200000
-    UNROLLED    : -k 15 -w 15    -o 2 -O 32 -e 1 -E 0 -A 1 -B 2 -z 200 -Z 100 -r 2000   -L 0.5 -g 10000
-    )");
+    UNROLLED    : -k 15 -w 15    -o 2 -O 32 -e 1 -E 0 -A 1 -B 2 -z 200 -Z 100 -r 2000   -L 0.5 -g 10000)");
 
     // clang-format on
     return i;

diff --git a/src/IndexSettings.cpp b/src/IndexSettings.cpp
@@ -114,8 +114,7 @@ PacBio::CLI_v2::Interface IndexSettings::CreateCLI()
     SUBREAD     : -k 19 -w 10
     CCS or HiFi : -k 19 -w 10 -u
     ISOSEQ      : -k 15 -w 5  -u
-    UNROLLED    : -k 15 -w 15
-    )");
+    UNROLLED    : -k 15 -w 15)");
 
     // clang-format on
     return i;

diff --git a/src/main.cpp b/src/main.cpp
@@ -45,8 +45,7 @@ R"(Typical workflows:
      $ pbmm2 align hg38.mmi movie1.subreadset.xml | samtools sort > hg38.movie1.sorted.bam
 
   E. Align CCS fastq input and sort on-the-fly
-     $ pbmm2 align ref.fasta movie.Q20.fastq ref.movie.bam --preset CCS --sort --rg '@RG\tID:myid\tSM:mysample'
-)");
+     $ pbmm2 align ref.fasta movie.Q20.fastq ref.movie.bam --preset CCS --sort --rg '@RG\tID:myid\tSM:mysample')");
 
     // clang-format on
     return mi;