From 4837fe919cb35e6d7db9ae3c0e99f00e8a5978b3 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 23 Nov 2009 22:46:05 +0000 Subject: [PATCH] Convenience changes. If no -BWT option is specified, pull the BWT location from the reference. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2130 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/alignment/AlignmentValidationWalker.java | 4 +++- .../broadinstitute/sting/alignment/AlignmentWalker.java | 8 +++++--- .../sting/alignment/CountBestAlignmentsWalker.java | 4 +++- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java index 667ed47a1..116803ed6 100644 --- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java @@ -22,7 +22,7 @@ public class AlignmentValidationWalker extends ReadWalker { * The supporting BWT index generated using BWT. */ @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false) - String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta"; + private String prefix = null; /** * The instance used to generate alignments. @@ -34,6 +34,8 @@ public class AlignmentValidationWalker extends ReadWalker { */ @Override public void initialize() { + if(prefix == null) + prefix = getToolkit().getArguments().referenceFile.getAbsolutePath(); BWTFiles bwtFiles = new BWTFiles(prefix); BWAConfiguration configuration = new BWAConfiguration(); aligner = new BWACAligner(bwtFiles,configuration); diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java index 6127c7ac9..8fb2f5061 100644 --- a/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java +++ b/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java @@ -20,13 +20,13 @@ import java.io.File; @WalkerName("Align") public class AlignmentWalker extends ReadWalker { @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false) - String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta"; + private String prefix = null; @Argument(fullName = "outputBam", shortName = "ob", doc = "Write output to this BAM filename instead of STDOUT", required = false) - String outputBamFile = null; + private String outputBamFile = null; @Argument(fullName = "bam_compression", shortName = "compress", doc = "Compression level to use for writing BAM files", required = false) - Integer bamCompression = 5; + private Integer bamCompression = 5; /** * The actual aligner. @@ -56,6 +56,8 @@ public class AlignmentWalker extends ReadWalker { */ @Override public void initialize() { + if(prefix == null) + prefix = getToolkit().getArguments().referenceFile.getAbsolutePath(); BWTFiles bwtFiles = new BWTFiles(prefix); BWAConfiguration configuration = new BWAConfiguration(); aligner = new BWACAligner(bwtFiles,configuration); diff --git a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java index 3fdd46952..30d892d71 100644 --- a/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java +++ b/java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java @@ -20,7 +20,7 @@ public class CountBestAlignmentsWalker extends ReadWalker { * The supporting BWT index generated using BWT. */ @Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false) - String prefix = "/Users/mhanna/reference/Ecoli/Escherichia_coli_K12_MG1655.fasta"; + private String prefix = null; /** * The actual aligner. @@ -34,6 +34,8 @@ public class CountBestAlignmentsWalker extends ReadWalker { */ @Override public void initialize() { + if(prefix == null) + prefix = getToolkit().getArguments().referenceFile.getAbsolutePath(); BWTFiles bwtFiles = new BWTFiles(prefix); BWAConfiguration configuration = new BWAConfiguration(); aligner = new BWACAligner(bwtFiles,configuration);