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Let's make artificial reads that actually adhere to the specs... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3022 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-17 16:51:42 +00:00
parent 5b34bb9ab0
commit ded4ba8966
2 changed files with 7 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
View File

@ -155,12 +155,14 @@ public class ArtificialSAMUtils {
record.setCigar(new Cigar(elements)); record.setCigar(new Cigar(elements));
record.setProperPairFlag(false); record.setProperPairFlag(false);
// our reads are all 'A's by default // our reads and quals are all 'A's by default
byte[] c = new byte[length]; byte[] c = new byte[length];
byte[] q = new byte[length];
for (int x = 0; x < length; x++) for (int x = 0; x < length; x++)
c[x] = 'A'; c[x] = q[x] = 'A';
record.setReadBases(c); record.setReadBases(c);
record.setBaseQualities(q);
if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) { if (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
record.setReadUmappedFlag(true); record.setReadUmappedFlag(true);
} }

3
java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -55,7 +55,8 @@ public class GATKSAMRecord extends SAMRecord {
setAttribute(attribute.tag, attribute.value); setAttribute(attribute.tag, attribute.value);
// if we are using original quals, set them now if t hey are present in the record // if we are using original quals, set them now if t hey are present in the record
if ( GenomeAnalysisEngine.instance.getArguments().useOriginalBaseQualities ) { if ( GenomeAnalysisEngine.instance != null &&
GenomeAnalysisEngine.instance.getArguments().useOriginalBaseQualities ) {
byte[] originalQuals = mRecord.getOriginalBaseQualities(); byte[] originalQuals = mRecord.getOriginalBaseQualities();
if ( originalQuals != null ) if ( originalQuals != null )
mRecord.setBaseQualities(originalQuals); mRecord.setBaseQualities(originalQuals);