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Comments for Mauricio 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5275 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-18 16:58:34 +00:00
parent 52f860c9b2
commit d97ed3e080
1 changed files with 15 additions and 9 deletions
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24
scala/qscript/oneoffs/carneiro/dataProcessing.scala
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@ -15,6 +15,8 @@ class dataProcessing extends QScript {
@Input(doc="path to AnalyzeCovariates.jar", shortName="ac", required=true)
var ACJar: File = _
// todo -- we should support the standard GATK arguments -R, -D [dbsnp],
// todo -- and indel files. Those should be defaulted to hg19 but providable on command line
@Input(doc="path to R resources folder inside Sting", shortName="r", required=true)
var R: String = _
@ -36,6 +38,7 @@ class dataProcessing extends QScript {
@Input(doc="the -L interval string to be used by GATK", shortName="L", required=false)
var intervalString: String = ""
// todo -- this shouldn't be allowed. We want a flag that says "output bams at intervals only" or not
@Input(doc="provide a .intervals file with the list of target intervals", shortName="intervals", required=false)
var intervals: File = new File("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals")
@ -43,6 +46,8 @@ class dataProcessing extends QScript {
// Reference sequence, dbsnps and RODs used by the pipeline
val reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
// TODO -- let's create a pre-merged single VCF and put it into /humgen/gsa-hpprojects/GATK/data please
val dindelPilotCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg.pilot_release.merged.indels.sites.hg19.vcf"
val dindelAFRCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/AFR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/ASN.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
@ -52,7 +57,6 @@ class dataProcessing extends QScript {
val knownsOnly: Boolean = true
val intermediate: Boolean = true
// General arguments to all programs
trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.GATKjar
@ -100,13 +104,13 @@ class dataProcessing extends QScript {
val postOutPath: String = baseName + ".post"
add(new target(perLaneBam, targetIntervals),
new clean(perLaneBam, targetIntervals, cleanedBam, knownsOnly),
new fixMates(cleanedBam, fixedBam, intermediate),
new dedup(fixedBam, dedupedBam, metricsFile),
new index(dedupedBam),
new clean(perLaneBam, targetIntervals, cleanedBam, knownsOnly), // todo -- use constrained movement mode to skip this
new fixMates(cleanedBam, fixedBam, intermediate), // todo -- use constrained movement mode to skip this
new dedup(fixedBam, dedupedBam, metricsFile), // todo -- generate index on fly here
new index(dedupedBam), // todo -- remove for on the fly index
new cov(dedupedBam, preRecalFile),
new recal(dedupedBam, preRecalFile, recalBam),
new index(recalBam),
new recal(dedupedBam, preRecalFile, recalBam), // todo -- use GATK on the fly indexing?
new index(recalBam), // todo remove for on the fly indexing
new cov(recalBam, postRecalFile),
new analyzeCovariates(preRecalFile, preOutPath),
new analyzeCovariates(postRecalFile, postOutPath))
@ -129,8 +133,8 @@ class dataProcessing extends QScript {
add(new writeList(recalibratedBamList, bamList, recalibratedBamIndexList),
new target(bamList, targetIntervals),
new clean(bamList, targetIntervals, cleanedBam, !knownsOnly),
new fixMates(cleanedBam, fixedBam, !intermediate))
new clean(bamList, targetIntervals, cleanedBam, !knownsOnly), // todo -- use constrained movement mode to skip fix mates
new fixMates(cleanedBam, fixedBam, !intermediate)) // todo -- use constrained movement mode to skip this
}
class target (inBams: String, outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
@ -188,6 +192,8 @@ class dataProcessing extends QScript {
this.jobName = inBam + ".dedup"
}
// todo -- may we should use the picard version instead? What about telling all of the picard tools to
// todo -- generate BAM indices on the fly? That would be even better
class index (inBam: String) extends SamtoolsIndexFunction {
@Output(doc="bam index file") var outIndex: File = new File(inBam + ".bai")
this.bamFile = new File(inBam)