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Add hidden option to ValidationAmplicons to output slightly modified format to make file work with downstream SQNM tools more seamlessly at request of GAP: one line per record, keep probe identifier to 20 characters, no * in ref allele.

This commit is contained in:
Guillermo del Angel 2011-11-11 14:07:07 -05:00
parent 40fbeafa37
commit cd3146f4cf
1 changed files with 14 additions and 5 deletions
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19
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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@ -7,10 +7,7 @@ import org.broadinstitute.sting.alignment.Alignment;
import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
import org.broadinstitute.sting.alignment.bwa.BWTFiles; import org.broadinstitute.sting.alignment.bwa.BWTFiles;
import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@ -126,6 +123,11 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
@Argument(doc="Do not use BWA, lower-case repeats only",fullName="doNotUseBWA",required=false) @Argument(doc="Do not use BWA, lower-case repeats only",fullName="doNotUseBWA",required=false)
boolean doNotUseBWA = false; boolean doNotUseBWA = false;
@Hidden
@Argument(doc="Use Sequenom output format instead of regular FASTA",fullName="sqnm",required=false)
boolean sequenomOutput = false;
GenomeLoc prevInterval; GenomeLoc prevInterval;
GenomeLoc allelePos; GenomeLoc allelePos;
String probeName; String probeName;
@ -485,6 +487,13 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
} }
String seqIdentity = sequence.toString().replace('n', 'N').replace('i', 'I').replace('d', 'D'); String seqIdentity = sequence.toString().replace('n', 'N').replace('i', 'I').replace('d', 'D');
out.printf(">%s %s %s%n%s%n", allelePos != null ? allelePos.toString() : "multiple", valid, probeName, seqIdentity);
if (!sequenomOutput)
out.printf(">%s %s %s%n%s%n", allelePos != null ? allelePos.toString() : "multiple", valid, probeName, seqIdentity);
else {
seqIdentity = seqIdentity.replace("*",""); // identifier < 20 letters long, no * in ref allele, one line per record
probeName = probeName.replace("amplicon_","a");
out.printf("%s_%s %s%n", allelePos != null ? allelePos.toString() : "multiple", probeName, seqIdentity);
}
} }
} }