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

Merge pull request #209 from broadinstitute/eb_more_fixes_to_bundle_script 

Now that we don't generate dict and fai files, the resource script needs...
This commit is contained in:
Eric Banks 2013-05-02 12:23:41 -07:00
parent 13bfa963da d981fd01b8
commit c6df20cff5
1 changed files with 15 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

25
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
View File

@ -234,8 +234,7 @@ class GATKResourcesBundle extends QScript {
for ( resource: Resource <- RESOURCES ) { for ( resource: Resource <- RESOURCES ) {
if ( isFASTA(resource.file) ) { if ( isFASTA(resource.file) ) {
val f = copyBundleFile(resource, resource.ref) copyBundleFasta(resource, resource.ref)
add(new createDictandFAI(f))
} else if ( isBAM(resource.file) ) { } else if ( isBAM(resource.file) ) {
val f = copyBundleFile(resource, resource.ref) val f = copyBundleFile(resource, resource.ref)
add(new IndexBAM(f)) add(new IndexBAM(f))
@ -312,6 +311,20 @@ class GATKResourcesBundle extends QScript {
} }
} }
def copyBundleFasta(res: Resource, ref: Reference) {
val out = destFile(BUNDLE_DIR, ref, res.destname(ref))
add(new cpFile(res.file, out))
val oldRefDict = swapExt(res.file.getParent, res.file, ".fasta", ".dict")
val newRefDict = swapExt(out.getParent, out, ".fasta", ".dict")
val oldRefFai = swapExt(res.file.getParent, res.file, ".fasta", ".fasta.fai")
val newRefFai = swapExt(out.getParent, out, ".fasta", ".fasta.fai")
add(new cpFile(oldRefDict, newRefDict))
add(new cpFile(oldRefFai, newRefFai))
}
def copyBundleFile(res: Resource, ref: Reference): File = { def copyBundleFile(res: Resource, ref: Reference): File = {
val out = destFile(BUNDLE_DIR, ref, res.destname(ref)) val out = destFile(BUNDLE_DIR, ref, res.destname(ref))
add(new cpFile(res.file, out)) add(new cpFile(res.file, out))
@ -389,13 +402,5 @@ class GATKResourcesBundle extends QScript {
else else
return ""; return "";
} }
class createDictandFAI (@Input ref: File) extends FastaStats with UNIVERSAL_GATK_ARGS {
@Output val outDict: File = swapExt(ref.getParent, ref, ".fasta", ".dict")
@Output val outFai: File = swapExt(ref.getParent, ref, ".fasta", ".fasta.fai")
@Output val outStats: File = swapExt(ref.getParent, ref, ".fasta", ".stats")
this.reference_sequence = ref
this.out = outStats
}
} }