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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
This commit is contained in:
hanna 2009-11-23 22:46:05 +00:00
parent 9e4eadc37c
commit 4837fe919c
3 changed files with 11 additions and 5 deletions
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4
java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
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@ -22,7 +22,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
* The supporting BWT index generated using BWT. * The supporting BWT index generated using BWT.
*/ */
@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false) @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. * The instance used to generate alignments.
@ -34,6 +34,8 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
*/ */
@Override @Override
public void initialize() { public void initialize() {
if(prefix == null)
prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
BWTFiles bwtFiles = new BWTFiles(prefix); BWTFiles bwtFiles = new BWTFiles(prefix);
BWAConfiguration configuration = new BWAConfiguration(); BWAConfiguration configuration = new BWAConfiguration();
aligner = new BWACAligner(bwtFiles,configuration); aligner = new BWACAligner(bwtFiles,configuration);

8
java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java
View File

@ -20,13 +20,13 @@ import java.io.File;
@WalkerName("Align") @WalkerName("Align")
public class AlignmentWalker extends ReadWalker<Integer,Integer> { public class AlignmentWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false) @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) @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) @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. * The actual aligner.
@ -56,6 +56,8 @@ public class AlignmentWalker extends ReadWalker<Integer,Integer> {
*/ */
@Override @Override
public void initialize() { public void initialize() {
if(prefix == null)
prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
BWTFiles bwtFiles = new BWTFiles(prefix); BWTFiles bwtFiles = new BWTFiles(prefix);
BWAConfiguration configuration = new BWAConfiguration(); BWAConfiguration configuration = new BWAConfiguration();
aligner = new BWACAligner(bwtFiles,configuration); aligner = new BWACAligner(bwtFiles,configuration);

4
java/src/org/broadinstitute/sting/alignment/CountBestAlignmentsWalker.java
View File

@ -20,7 +20,7 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
* The supporting BWT index generated using BWT. * The supporting BWT index generated using BWT.
*/ */
@Argument(fullName="BWTPrefix",shortName="BWT",doc="Index files generated by bwa index -d bwtsw",required=false) @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. * The actual aligner.
@ -34,6 +34,8 @@ public class CountBestAlignmentsWalker extends ReadWalker<Integer,Integer> {
*/ */
@Override @Override
public void initialize() { public void initialize() {
if(prefix == null)
prefix = getToolkit().getArguments().referenceFile.getAbsolutePath();
BWTFiles bwtFiles = new BWTFiles(prefix); BWTFiles bwtFiles = new BWTFiles(prefix);
BWAConfiguration configuration = new BWAConfiguration(); BWAConfiguration configuration = new BWAConfiguration();
aligner = new BWACAligner(bwtFiles,configuration); aligner = new BWACAligner(bwtFiles,configuration);