zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add the ability to extract samples

This commit is contained in:
Christopher Hartl 2012-02-02 09:06:39 -05:00
parent b567ed8793
commit f8c5406084
1 changed files with 19 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/lib/VcfToPed.scala
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.queue.library.ipf.vcf.VCFExtractIntervals
import org.broadinstitute.sting.utils.text.XReadLines import org.broadinstitute.sting.utils.text.XReadLines
import collection.JavaConversions._ import collection.JavaConversions._
import java.io._ import java.io._
import org.broadinstitute.sting.queue.extensions.gatk.VariantsToPed import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, VariantsToPed}
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
@ -36,6 +36,9 @@ class VcfToPed extends QScript {
@Argument(shortName="D",fullName="dbsnp",required=false,doc="dbsnp file") @Argument(shortName="D",fullName="dbsnp",required=false,doc="dbsnp file")
var dbsnp : File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b37.vcf") var dbsnp : File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b37.vcf")
@Argument(shortName="sf",fullName="sampleFile",required=false,doc="sample file")
var samFile : File = _
val tmpdir : File = System.getProperty("java.io.tmpdir") val tmpdir : File = System.getProperty("java.io.tmpdir")
def script = { def script = {
@ -59,9 +62,22 @@ class VcfToPed extends QScript {
val toPed : VariantsToPed = new VariantsToPed val toPed : VariantsToPed = new VariantsToPed
toPed.memoryLimit = 2 toPed.memoryLimit = 2
toPed.reference_sequence = ref toPed.reference_sequence = ref
toPed.intervals :+= new File(subListFile) toPed.intervals :+= subListFile
toPed.dbsnp = dbsnp toPed.dbsnp = dbsnp
toPed.variant = variants if ( samFile != null ) {
val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk)
val extract : SelectVariants = new SelectVariants
extract.reference_sequence = ref
extract.memoryLimit = 2
extract.intervals :+= subListFile
extract.variant = variants
extract.out = new File(tmpdir,base+"_extract%d.vcf".format(chunk))
extract.sample_file :+= samFile
add(extract)
toPed.variant = extract.out
} else {
toPed.variant = variants
}
toPed.metaData = meta toPed.metaData = meta
val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk) val base : String = bed.getName.stripSuffix(".bed")+"_%d".format(chunk)
val tBed = new File(tmpdir,base+".bed") val tBed = new File(tmpdir,base+".bed")