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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-02-22 19:00:38 -05:00
parent 8695738400 2c1b14d35e
commit 2b6c0939ab
3 changed files with 26 additions and 10 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToPed.java
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@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -45,6 +46,9 @@ public class VariantsToPed extends RodWalker<Integer,Integer> {
@Output(shortName="fam",fullName="fam",required=true,doc="output fam file")
PrintStream outFam;
@Argument(shortName="mgq",fullName="minGenotypeQuality",required=true,doc="If genotype quality is lower than this value, output NO_CALL")
int minGenotypeQuality = 0;
private ValidateVariants vv = new ValidateVariants();
private static double APPROX_CM_PER_BP = 1000000.0/750000.0;
@ -173,9 +177,11 @@ public class VariantsToPed extends RodWalker<Integer,Integer> {
return 0;
}
private static byte getEncoding(Genotype g, int offset) {
private byte getEncoding(Genotype g, int offset) {
byte b;
if ( g.isHomRef() ) {
if ( g.hasAttribute(VCFConstants.GENOTYPE_QUALITY_KEY) && ((Integer) g.getAttribute(VCFConstants.GENOTYPE_QUALITY_KEY)) < minGenotypeQuality ) {
b = NO_CALL;
} else if ( g.isHomRef() ) {
b = HOM_REF;
} else if ( g.isHomVar() ) {
b = HOM_VAR;

12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/ChunkVCF.scala
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@ -23,7 +23,7 @@ class ChunkVCF extends QScript {
@Input(shortName="N",fullName="numEntriesInChunk",doc="The number of variants per chunk",required=true)
var numEntries : Int = _
@Input(shortName="I",fullName="Intervals",doc="The SNP interval list to chunk. If not provided, one will be created for you to provide in a second run.")
@Input(shortName="I",fullName="Intervals",doc="The SNP interval list to chunk. If not provided, one will be created for you to provide in a second run.",required=false)
var intervals : File = _
@Input(fullName="preserveChromosomes",doc="Restrict chunks to one chromosome (smaller chunk at end of chromosome)",required=false)
@ -40,8 +40,8 @@ class ChunkVCF extends QScript {
def script = {
if ( intervals == null ) {
// create an interval list from the VCF
val ivals : File = swapExt(variants,".vcf",".intervals.list")
val extract : VCFExtractIntervals = new VCFExtractIntervals(variants,ivals,false)
val ivals : File = swapExt(inVCF,".vcf",".intervals.list")
val extract : VCFExtractIntervals = new VCFExtractIntervals(inVCF,ivals,false)
add(extract)
} else {
var chunkNum = 1
@ -54,11 +54,12 @@ class ChunkVCF extends QScript {
if ( ( preserve && ! int.split(":")(0).equals(chromosome) ) || numLinesInChunk > numEntries ) {
chunkWriter.close()
val chunkSelect : SelectVariants = new SelectVariants
chunkSelect.variant = inVCF
chunkSelect.reference_sequence = ref
chunkSelect.memoryLimit = 2
chunkSelect.intervals :+= chunkFile
if ( extractSamples != null )
chunkSelect.sample_file = extractSamples
chunkSelect.sample_file :+= extractSamples
chunkSelect.out = swapExt(inVCF,".vcf",".chunk%d.vcf".format(chunkNum))
add(chunkSelect)
chunkNum += 1
@ -74,12 +75,13 @@ class ChunkVCF extends QScript {
if ( numLinesInChunk > 0 ) {
// some work to do
val chunkSelect : SelectVariants = new SelectVariants
chunkSelect.variant = inVCF
chunkSelect.reference_sequence = ref
chunkSelect.memoryLimit = 2
chunkSelect.intervals :+= chunkFile
chunkWriter.close()
if ( extractSamples != null )
chunkSelect.sample_file = extractSamples
chunkSelect.sample_file :+= extractSamples
chunkSelect.out = swapExt(inVCF,".vcf",".chunk%d.vcf".format(chunkNum))
add(chunkSelect)
}

14
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala
View File

@ -47,9 +47,14 @@ class VcfToPed extends QScript {
val extract : VCFExtractIntervals = new VCFExtractIntervals(variants,ivals,false)
add(extract)
} else {
val IS_GZ : Boolean = variants.getName.endsWith(".vcf.gz")
var iXRL = new XReadLines(intervals)
var chunk = 1;
var subListFile = swapExt(tmpdir,variants,".vcf",".chunk%d.list".format(chunk))
var subListFile : File = null
if ( IS_GZ )
subListFile = swapExt(tmpdir,variants,".vcf.gz",".chunk%d.list".format(chunk))
else
subListFile = swapExt(tmpdir,variants,".vcf",".chunk%d.list".format(chunk))
var subList = new PrintStream(subListFile)
var nL = 0;
var bedOuts : List[File] = Nil;
@ -58,7 +63,7 @@ class VcfToPed extends QScript {
while ( iXRL.hasNext ) {
subList.printf("%s%n",iXRL.next())
nL = nL + 1
if ( nL > 100000 ) {
if ( nL > 10000 ) {
val toPed : VariantsToPed = new VariantsToPed
toPed.memoryLimit = 2
toPed.reference_sequence = ref
@ -89,7 +94,10 @@ class VcfToPed extends QScript {
add(toPed)
subList.close()
chunk = chunk + 1
subListFile = swapExt(tmpdir,variants,".vcf",".chunk%d.list".format(chunk))
if ( IS_GZ )
subListFile = swapExt(tmpdir,variants,".vcf.gz",".chunk%d.list".format(chunk))
else
subListFile = swapExt(tmpdir,variants,".vcf",".chunk%d.list".format(chunk))
subList = new PrintStream(subListFile)
bedOuts :+= tBed
bimOuts :+= bim