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

Queue graph time is currently of O(n^m) where n = num jobs, m = num unique base files. This script therefore was running in order 1200^16, which I don't think would finish before the heat death of the universe. For now, push down the number of files to 1 and gather them outside of Queue, once I've fixed up scatter-gather in core, outputs can be uncommented. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5674 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-04-21 12:56:25 +00:00
parent 9f006be425
commit 5b9a8555cd
2 changed files with 16 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
java/src/org/broadinstitute/sting/oneoffprojects/walkers/association/RAWSampleStats.java
View File

@ -51,19 +51,23 @@ public class RAWSampleStats extends LocusWalker<MapHolder,RegionalAssociationHan
for ( AssociationContext context : handler.getAssociations() ) {
contextBuf.append("\t");
contextBuf.append(context.getClass().getSimpleName());
StringBuffer caseBuf = new StringBuffer();
StringBuffer controlBuf = new StringBuffer();
boolean first = true;
for ( Map.Entry<Sample,AlignmentContext> entry : handler.getExtender().getContext().entrySet() ) {
if ( ! first ) {
contextBuf.append(";");
} else {
contextBuf.append("\t");
first = false;
}
contextBuf.append(entry.getKey().getId());
contextBuf.append("=");
contextBuf.append(handleMap(context.map(entry.getValue().getBasePileup())));
StringBuffer toAppend = entry.getKey().getProperty("cohort").equals("case") ? caseBuf : controlBuf;
toAppend.append(entry.getKey().getId());
toAppend.append("=");
toAppend.append(handleMap(context.map(entry.getValue().getBasePileup())));
toAppend.append(";");
}
caseBuf.deleteCharAt(caseBuf.length()-1);
controlBuf.deleteCharAt(controlBuf.length()-1);
contextBuf.append("\t");
contextBuf.append("Case:\t");
contextBuf.append(caseBuf);
contextBuf.append("\tControl:\t");
contextBuf.append(controlBuf);
}
out.printf("%s%n",contextBuf.toString());

4
scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
View File

@ -41,6 +41,7 @@ class ScatterGatherAssociation extends QScript {
@Output(doc="bqs")
@Gather(classOf[SimpleTextGatherFunction])
var bqs : File = new File(String.format("%s.%s.%s", base, "BaseQualityScore", ext))
/*
@Output(doc="isd")
@Gather(classOf[SimpleTextGatherFunction])
var isd : File = new File(String.format("%s.%s.%s",base,"InsertSizeDistribution",ext))
@ -56,7 +57,7 @@ class ScatterGatherAssociation extends QScript {
@Output(doc="mss")
@Gather(classOf[SimpleTextGatherFunction])
var mss : File = new File(String.format("%s.%s.%s",base,"MateSameStrand",ext))
@Output(doc="mu")
/@Output(doc="mu")
@Gather(classOf[SimpleTextGatherFunction])
var mu : File = new File(String.format("%s.%s.%s",base,"MateUnmapped",ext))
@Output(doc="mmr")
@ -86,6 +87,7 @@ class ScatterGatherAssociation extends QScript {
@Output(doc="rwi")
@Gather(classOf[SimpleTextGatherFunction])
var rwi : File = new File(String.format("%s.%s.%s",base,"ReadsWithIndels",ext))
*/
override def commandLine = {
var bedStr : String = ""