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

Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-07-13 14:57:33 -04:00
parent bb0e3a26fc e2f2917bd2
commit 0c54c796ed
2 changed files with 9 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -220,6 +220,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
else {
unprocessedList.add(vc); // Finished with the unprocessed variant, and writer can enforce sorting on-the-fly
if (DEBUG)
logger.debug("Unprocessed variant = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
}
int numReads = 0;
@ -1105,7 +1108,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
this.alleles = vc.getAlleles();
this.genotypes = new HashMap<String, Genotype>(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
this.negLog10PError = vc.getNegLog10PError();
this.filters = vc.getFilters();
this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
this.attributes = new HashMap<String, Object>(vc.getAttributes());
}

10
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
View File

@ -41,11 +41,11 @@ class RecalibrateBaseQualities extends QScript {
nContigs = getNumberOfContigs(input)
val recalFile1: File = swapExt(input, ".bam", "recal1.csv")
val recalFile2: File = swapExt(input, ".bam", "recal2.csv")
val recalBam: File = swapExt(input, ".bam", "recal.bam")
val path1: String = "before"
val path2: String = "after"
val recalFile1: File = swapExt(input, ".bam", ".recal1.csv")
val recalFile2: File = swapExt(input, ".bam", ".recal2.csv")
val recalBam: File = swapExt(input, ".bam", ".recal.bam")
val path1: String = input + "before"
val path2: String = input + "after"
add(cov(input, recalFile1),
recal(input, recalFile1, recalBam),