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Minor improvements in ref QC walker. Unfortunately this doesn't actually catch Chris's error

This commit is contained in:
Mark DePristo 2012-01-27 08:24:17 -05:00
parent cb04c0bf11
commit 13d1626f51
1 changed files with 26 additions and 4 deletions
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30
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRefWalker.java
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@ -83,7 +83,7 @@ public class QCRefWalker extends RefWalker<Integer, Integer> {
}
private final void throwError(ReferenceContext ref, String message) {
throw new StingException(String.format("Site %s failed: %s", ref, message));
throw new StingException(String.format("Site %s failed: %s", ref.getLocus(), message));
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@ -92,13 +92,13 @@ public class QCRefWalker extends RefWalker<Integer, Integer> {
contigName = locusContigName;
ReferenceSequence refSeq = uncachedRef.getSequence(contigName);
contigStart = 1;
contigEnd = contigStart + refSeq.length();
contigEnd = contigStart + refSeq.length() - 1;
uncachedBases = uncachedRef.getSubsequenceAt(contigName, contigStart, contigEnd).getBases();
logger.warn(String.format("Loading contig %s (%d-%d)", contigName, contigStart, contigEnd));
logger.info(String.format("Loading contig %s (%d-%d)", contigName, contigStart, contigEnd));
}
final byte refBase = ref.getBase();
if (! ( BaseUtils.isRegularBase(refBase) || BaseUtils.isNBase(refBase) ) )
if (! ( BaseUtils.isRegularBase(refBase) || isExtendFastaBase(refBase) ) )
throwError(ref, String.format("Refbase isn't a regular base (%d %c)", refBase, (char)refBase));
// check bases are equal
@ -114,6 +114,28 @@ public class QCRefWalker extends RefWalker<Integer, Integer> {
return 1;
}
private static final boolean isExtendFastaBase(final byte b) {
switch ( b ) {
case 'U':
case 'R':
case 'Y':
case 'K':
case 'M':
case 'S':
case 'W':
case 'B':
case 'D':
case 'H':
case 'V':
case 'N':
case 'X':
case '-':
return true;
default:
return false;
}
}
public Integer reduceInit() {
return 0;
}