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Moved extra walkers at Mark's request. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@96 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-03-18 23:52:08 +00:00
parent ffb6f8f5da
commit 225ea64bd9
3 changed files with 0 additions and 15 deletions
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0
playground/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java → core/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
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15
playground/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java → core/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -27,27 +27,16 @@ public class PileupWalker extends BasicLociWalker<Integer, Integer> {
// Map over the org.broadinstitute.sting.gatk.LocusContext // Map over the org.broadinstitute.sting.gatk.LocusContext
public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) { public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
//System.out.printf("Reads %s:%d %d%n", context.getContig(), context.getPosition(), context.getReads().size());
//for ( SAMRecord read : context.getReads() ) {
// System.out.println(" -> " + read.getReadName());
//}
List<SAMRecord> reads = context.getReads(); List<SAMRecord> reads = context.getReads();
List<Integer> offsets = context.getOffsets(); List<Integer> offsets = context.getOffsets();
String bases = ""; String bases = "";
String quals = ""; String quals = "";
//String offsetString = "";
for ( int i = 0; i < reads.size(); i++ ) { for ( int i = 0; i < reads.size(); i++ ) {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
int offset = offsets.get(i); int offset = offsets.get(i);
//if ( offset >= read.getReadString().length() )
// System.out.printf(" [%2d] [%s] %s%n", offset, read.format(), read.getReadString());
bases += read.getReadString().charAt(offset); bases += read.getReadString().charAt(offset);
quals += read.getBaseQualityString().charAt(offset); quals += read.getBaseQualityString().charAt(offset);
//offsetString += i;
//System.out.printf(" [%2d] [%s] %s%n", offset, read.getReadString().charAt(offset), read.getReadString());
} }
String rodString = ""; String rodString = "";
@ -55,7 +44,6 @@ public class PileupWalker extends BasicLociWalker<Integer, Integer> {
if ( datum != null ) { if ( datum != null ) {
if ( datum instanceof rodDbSNP) { if ( datum instanceof rodDbSNP) {
rodDbSNP dbsnp = (rodDbSNP)datum; rodDbSNP dbsnp = (rodDbSNP)datum;
//System.out.printf(" DBSNP %s on %s => %s%n", dbsnp.toSimpleString(), dbsnp.strand, Utils.join("/", dbsnp.getAllelesFWD()));
rodString += dbsnp.toMediumString(); rodString += dbsnp.toMediumString();
} }
else { else {
@ -70,9 +58,6 @@ public class PileupWalker extends BasicLociWalker<Integer, Integer> {
System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString); System.out.printf("%s: %s %s %s %s%n", context.getLocation(), ref, bases, quals, rodString);
} }
//for ( int offset : context.getOffsets() ) {
// System.out.println(" -> " + read.getReadName());
//}
return 1; return 1;
} }

0
playground/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java → core/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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