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make refseq annotation file an optional argument; if specified, indels will be annotated as genomic/utr/intron/coding (accidentally appearing 'unknowns' probably mean that there's something wrong with refseq annotations?) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1077 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-06-23 18:17:03 +00:00
parent 9c0dba6979
commit 1339f3f3e3
1 changed files with 25 additions and 4 deletions
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29
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
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@ -46,16 +46,20 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="minConsensusFraction", shortName="minConsensusFraction", @Argument(fullName="minConsensusFraction", shortName="minConsensusFraction",
doc="Minimum fraction of reads with indel at the site that must contain consensus indel in order to make the call", required=false) doc="Minimum fraction of reads with indel at the site that must contain consensus indel in order to make the call", required=false)
public double minConsensusFraction = 0.7; public double minConsensusFraction = 0.7;
@Argument(fullName="refseq", shortName="refseq",
doc="Name of RefSeq transcript annotation file. If specified, indels will be annotated as GENOMIC/UTR/INTRON/CODING", required=false)
public String RefseqFileName = null;
private static int WINDOW_SIZE = 200; private static int WINDOW_SIZE = 200;
private RunningCoverage coverage; private RunningCoverage coverage;
private RunningCoverage normal_coverage; // when performing somatic calls, we will be using this one for normal, and 'coverage' for tumor private RunningCoverage normal_coverage; // when performing somatic calls, we will be using this one for normal, and 'coverage' for tumor
private int currentContigIndex = -1; private int currentContigIndex = -1;
private int currentPosition = -1; // position of the last read we've seen on the current contig
private String refName = null; private String refName = null;
private java.io.Writer output = null; private java.io.Writer output = null;
private GenomeLoc location = null; private GenomeLoc location = null;
private RODIterator<rodRefSeq> refseqIterator; private RODIterator<rodRefSeq> refseqIterator=null;
private Set<String> normal_samples = new HashSet<String>(); private Set<String> normal_samples = new HashSet<String>();
private Set<String> tumor_samples = new HashSet<String>(); private Set<String> tumor_samples = new HashSet<String>();
@ -71,14 +75,20 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
private static String annCoding = "CODING"; private static String annCoding = "CODING";
private static String annUnknown = "UNKNOWN"; private static String annUnknown = "UNKNOWN";
private SAMRecord lastRead;
// "/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"
@Override @Override
public void initialize() { public void initialize() {
coverage = new RunningCoverage(0,WINDOW_SIZE); coverage = new RunningCoverage(0,WINDOW_SIZE);
ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq", if ( RefseqFileName != null ) {
new java.io.File("/humgen/gsa-scr1/GATK_Data/refGene.sorted.txt"),rodRefSeq.class); ReferenceOrderedData<rodRefSeq> refseq = new ReferenceOrderedData<rodRefSeq>("refseq",
new java.io.File(RefseqFileName),rodRefSeq.class);
refseqIterator = refseq.iterator(); refseqIterator = refseq.iterator();
}
int nSams = getToolkit().getArguments().samFiles.size(); int nSams = getToolkit().getArguments().samFiles.size();
@ -177,6 +187,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( call_somatic) emit_somatic(1000000000, true); // print remaining indels from the previous contig (if any); if ( call_somatic) emit_somatic(1000000000, true); // print remaining indels from the previous contig (if any);
else emit(1000000000,true); else emit(1000000000,true);
currentContigIndex = read.getReferenceIndex(); currentContigIndex = read.getReferenceIndex();
currentPosition = read.getAlignmentStart();
refName = new String(read.getReferenceName()); refName = new String(read.getReferenceName());
location.setContig(refName); location.setContig(refName);
@ -184,6 +195,14 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
if ( call_somatic) normal_coverage.clear(); if ( call_somatic) normal_coverage.clear();
} }
if ( read.getAlignmentStart() < currentPosition )
throw new StingException("Read "+read.getReadName() +" out of order on the contig\n"+
"Read starts at "+refName+":"+read.getAlignmentStart()+"; last read seen started at "+refName+":"+currentPosition
+"\nLast read was: "+lastRead.getReadName()+" RG="+lastRead.getAttribute("RG")+" at "+lastRead.getAlignmentStart()+"-"
+lastRead.getAlignmentEnd()+" cigar="+lastRead.getCigarString());
currentPosition = read.getAlignmentStart();
if ( read.getAlignmentStart() < coverage.getStart() ) { if ( read.getAlignmentStart() < coverage.getStart() ) {
// should never happen // should never happen
throw new StingException("Read "+read.getReadName()+": out of order on the contig\n"+ throw new StingException("Read "+read.getReadName()+": out of order on the contig\n"+
@ -191,6 +210,8 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
"); window starts at "+coverage.getStart()); "); window starts at "+coverage.getStart());
} }
lastRead = read;
// a little trick here: we want to make sure that current read completely fits into the current // a little trick here: we want to make sure that current read completely fits into the current
// window so that we can accumulate the coverage/indel counts over the whole length of the read. // window so that we can accumulate the coverage/indel counts over the whole length of the read.
// The ::getAlignmentEnd() method returns the last position on the reference where bases from the // The ::getAlignmentEnd() method returns the last position on the reference where bases from the