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Adding TODO notes for Ami

This commit is contained in:
Eric Banks 2012-10-26 13:20:27 -04:00
parent 46099af8db
commit a8704ca73f
1 changed files with 6 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
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@ -55,8 +55,8 @@ public class AssessReducedQuals extends LocusWalker<GenomeLoc, GenomeLoc> implem
@Argument(fullName = "qual_epsilon", shortName = "epsilon", doc = "when |Quals_reduced_bam - Quals_original_bam| > epsilon*Quals_original_bam we output this interval", required = false) @Argument(fullName = "qual_epsilon", shortName = "epsilon", doc = "when |Quals_reduced_bam - Quals_original_bam| > epsilon*Quals_original_bam we output this interval", required = false)
public int qual_epsilon = 0; public int qual_epsilon = 0;
@Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on") @Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on") // TODO -- best to make this optional
public int debugLevel = 0; public int debugLevel = 0; // TODO -- best to make this an enum or boolean
@Output @Output
protected PrintStream out; protected PrintStream out;
@ -114,7 +114,11 @@ public class AssessReducedQuals extends LocusWalker<GenomeLoc, GenomeLoc> implem
return quals; return quals;
} }
// TODO -- arguments/variables should be final, not method declaration
private final boolean isGoodRead(PileupElement p, List<String> tags){ private final boolean isGoodRead(PileupElement p, List<String> tags){
// TODO -- this isn't quite right. You don't need the tags here. Instead, you want to check whether the read itself (which
// TODO -- you can get from the PileupElement) is a reduced read (not all reads from the reduced bam are reduced) and only
// TODO -- for them do you want to ignore that min mapping quality cutoff (but you *do* still want the min base cutoff).
return !p.isDeletion() && (tags.contains(reduced) || (tags.contains(original) && (int)p.getQual() >= 20 && p.getMappingQual() >= 20)); return !p.isDeletion() && (tags.contains(reduced) || (tags.contains(original) && (int)p.getQual() >= 20 && p.getMappingQual() >= 20));
} }