zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Enable BAM OTF index writing by default. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5594 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-04-07 23:44:25 +00:00
parent cc58e19621
commit 32d502c122
2 changed files with 5 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java
View File

@ -51,7 +51,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
public static final String SIMPLIFY_BAM_FULLNAME = "simplifyBAM";
public static final String SIMPLIFY_BAM_SHORTNAME = SIMPLIFY_BAM_FULLNAME;
public static final String CREATE_INDEX_FULLNAME = "index_output_bam_on_the_fly";
public static final String CREATE_INDEX_FULLNAME = "disable_bam_indexing";
/**
* The engine into which output stubs should be fed.
@ -117,7 +117,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
if( compressionLevel != null )
stub.setCompressionLevel(compressionLevel);
stub.setIndexOnTheFly(argumentIsPresent(createWriteIndexArgumentDefinition(source),matches));
stub.setIndexOnTheFly(!argumentIsPresent(createWriteIndexArgumentDefinition(source),matches));
stub.setSimplifyBAM(argumentIsPresent(createSimplifyBAMArgumentDefinition(source),matches));
// WARNING: Side effects required by engine!
@ -176,7 +176,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
boolean.class,
CREATE_INDEX_FULLNAME,
null,
"Create a BAM index on-the-fly while writing the resulting file.",
"Turn off on-the-fly creation of indices for output BAM files.",
false,
false,
false,

4
java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
View File

@ -69,7 +69,7 @@ public class IntervalIntegrationTest extends WalkerTest {
" -I " + validationDataLocation + "MV1994.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -L unmapped" +
" -U --index_output_bam_on_the_fly",
" -U",
0, // two output files
Collections.<String>emptyList());
@ -89,7 +89,7 @@ public class IntervalIntegrationTest extends WalkerTest {
" -I " + validationDataLocation + "MV1994.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -XL unmapped" +
" -U --index_output_bam_on_the_fly",
" -U",
0, // two output files
Collections.<String>emptyList());