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Remember to take the strand flag into account when calculating error rate per cycle as a surrogate for instrument performance. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@347 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-09 20:48:45 +00:00
parent 8a1207e4db
commit d0ce56e018
1 changed files with 10 additions and 12 deletions
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22
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
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@ -80,24 +80,22 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
}
if (nextBestBase != '.') {
errorsPerCycle[cycle] = !(bases[cycle] == compBase || nextBestBase == compBase);
totalMismatches = (!(bases[cycle] == compBase || nextBestBase == compBase)) ? 1 : 0;
if (read.getReadNegativeStrandFlag()) {
errorsPerCycle[bases.length - cycle - 1] = !(bases[cycle] == compBase || nextBestBase == compBase);
} else {
errorsPerCycle[cycle] = !(bases[cycle] == compBase || nextBestBase == compBase);
}
}
} else {
errorsPerCycle[cycle] = !(bases[cycle] == compBase);
totalMismatches += (!(bases[cycle] == compBase)) ? 1 : 0;
if (read.getReadNegativeStrandFlag()) {
errorsPerCycle[bases.length - cycle - 1] = !(bases[cycle] == compBase);
} else {
errorsPerCycle[cycle] = !(bases[cycle] == compBase);
}
}
}
}
/*
if (totalMismatches > 4) {
for (int cycle = 0; cycle < bases.length; cycle++) { System.out.print((char) bases[cycle]); } System.out.print("\n");
for (int cycle = 0, offset = (int) context.getPosition(); cycle < bases.length; cycle++, offset++) { System.out.print((char) contig[offset]); } System.out.print("\n");
System.out.println(totalMismatches + "\n");
}
*/
// We encode that we saw a read in the last position of the array.
// That way we know what to normalize by, and we get thread safety!
errorsPerCycle[errorsPerCycle.length - 1] = true;