From cd3146f4cff4bc81aee7fd728dfb9c9a080e4247 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Fri, 11 Nov 2011 14:07:07 -0500 Subject: [PATCH] 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. --- .../validation/ValidationAmplicons.java | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java index 035d8d2ca..088c4ddc4 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java @@ -7,10 +7,7 @@ import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWTFiles; import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; -import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.commandline.Input; -import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.commandline.RodBinding; +import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; @@ -126,6 +123,11 @@ public class ValidationAmplicons extends RodWalker { @Argument(doc="Do not use BWA, lower-case repeats only",fullName="doNotUseBWA",required=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 allelePos; String probeName; @@ -485,6 +487,13 @@ public class ValidationAmplicons extends RodWalker { } 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); + } } }