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0.2.3 -- now preserves Q0 bases throughout the reads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1232 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-14 12:27:31 +00:00
parent 36819ed908
commit 5bf7647498
1 changed files with 21 additions and 2 deletions
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23
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -49,12 +49,15 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
@Argument(shortName="outputBAM", doc="output BAM file", required=false)
public String outputBamFile = null;
@Argument(shortName="rawQempirical", doc="If provide, we will use raw Qempirical scores calculated from the # mismatches and # bases, rather than the more conservative estimate of # mismatches + 1 / # bases + 1", required=false)
@Argument(shortName="rawQempirical", doc="If provided, we will use raw Qempirical scores calculated from the # mismatches and # bases, rather than the more conservative estimate of # mismatches + 1 / # bases + 1", required=false)
public boolean rawQempirical = false;
@Argument(shortName="adjustQ0Bases", doc="If provided, Q0 bases will have their quality scores modified, otherwise they will be left as Q0 in the output", required=false)
public boolean adjustQ0Bases = false;
private static Logger logger = Logger.getLogger(TableRecalibrationWalker.class);
private static String VERSION = "0.2.2";
private static String VERSION = "0.2.3";
private final static boolean DEBUG = false;
@ -249,6 +252,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
if (read.getReadNegativeStrandFlag()) // reverse the quals for the neg strand read
recalQuals = BaseUtils.reverse(recalQuals);
// special case the first and last bases in SOLID reads, which are always 0
// We actually just never change Q0 bases
preserveQ0Bases(quals, recalQuals, read);
read.setBaseQualities(recalQuals);
return read;
} catch ( StingException e ) {
@ -256,6 +263,18 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
}
}
private void preserveQ0Bases( byte[] originalQuals, byte[] recalQuals, SAMRecord read ) {
if ( ! adjustQ0Bases ) {
for ( int i = 0; i < recalQuals.length; i++ ) {
//System.out.printf("Original qual %d => %d%n", originalQuals[i], recalQuals[i]);
if ( originalQuals[i] == 0 ) {
//System.out.printf("Preserving Q0 base at %d in read %s%n", i, read.getReadName());
recalQuals[i] = 0;
}
}
}
}
/**
* Workhorse routine. Given a read group and an array of bases and quals, returns a new set of recalibrated
* qualities for each base/qual in bases and quals. Uses the RecalMapping object associated with readGroup.