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Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-11-01 00:33:18 +00:00
parent 4b0796ba58
commit b95165e39c
2 changed files with 22 additions and 3 deletions
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5
build.xml
View File

@ -104,7 +104,10 @@
</jar> </jar>
<jar jarfile="${dist}/GenomeAnalysisTK.jar"> <jar jarfile="${dist}/GenomeAnalysisTK.jar">
<fileset dir="build" includes="**/gatk/**/*.class"/> <fileset dir="build">
<include name="**/gatk/**/*.class"/>
<include name="**/alignment/**/*.class"/>
</fileset>
<manifest> <manifest>
<attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK"/> <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK"/>
</manifest> </manifest>

20
java/src/org/broadinstitute/sting/alignment/bwa/AlignmentValidationWalker.java
View File

@ -61,13 +61,29 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
matches &= (alignment.getAlignmentStart() == read.getAlignmentStart()); matches &= (alignment.getAlignmentStart() == read.getAlignmentStart());
matches &= (alignment.isNegativeStrand() == read.getReadNegativeStrandFlag()); matches &= (alignment.isNegativeStrand() == read.getReadNegativeStrandFlag());
matches &= (alignment.getCigar().equals(read.getCigar())); matches &= (alignment.getCigar().equals(read.getCigar()));
matches &= (alignment.getMappingQuality() == read.getMappingQuality()); //matches &= (alignment.getMappingQuality() == read.getMappingQuality());
if(matches) break; if(matches) break;
} }
} }
if(!matches) if(!matches) {
logger.error("Found mismatch!");
logger.error(String.format("Read %s:",read.getReadName()));
logger.error(String.format(" Contig index: %d",read.getReferenceIndex()));
logger.error(String.format(" Alignment start: %d", read.getAlignmentStart()));
logger.error(String.format(" Negative strand: %b", read.getReadNegativeStrandFlag()));
logger.error(String.format(" Cigar: %s%n", read.getCigarString()));
logger.error(String.format(" Mapping quality: %s%n", read.getMappingQuality()));
for(int i = 0; i < alignments.length; i++) {
logger.error(String.format("Alignment %d:",i));
logger.error(String.format(" Contig index: %d",alignments[i].getContigIndex()));
logger.error(String.format(" Alignment start: %d", alignments[i].getAlignmentStart()));
logger.error(String.format(" Negative strand: %b", alignments[i].isNegativeStrand()));
logger.error(String.format(" Cigar: %s", alignments[i].getCigarString()));
logger.error(String.format(" Mapping quality: %s%n", alignments[i].getMappingQuality()));
}
throw new StingException(String.format("Read %s mismatches!", read.getReadName())); throw new StingException(String.format("Read %s mismatches!", read.getReadName()));
}
return 1; return 1;
} }