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Merge branch 'master' into diffit

This commit is contained in:
Mark DePristo 2011-07-11 23:16:15 -04:00
parent 893cc2e103 d11155ce2e
commit d5056ad899
5 changed files with 32 additions and 26 deletions
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0
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableCodec.java 100644 → 100755
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6
public/java/src/org/broadinstitute/sting/gatk/refdata/features/table/TableFeature.java 100644 → 100755
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@ -55,10 +55,14 @@ public class TableFeature implements Feature {
} }
public List<String> getAllValues() { public List<String> getAllValues() {
return getValuesTo(values.size()-1); return getValuesTo(values.size());
} }
public List<String> getValuesTo(int columnPosition) { public List<String> getValuesTo(int columnPosition) {
return values.subList(0,columnPosition); return values.subList(0,columnPosition);
} }
public List<String> getHeader() {
return keys;
}
} }

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
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@ -108,7 +108,7 @@ public class Allele implements Comparable<Allele> {
this.bases = bases; this.bases = bases;
if ( ! acceptableAlleleBases(bases) ) if ( ! acceptableAlleleBases(bases) )
throw new IllegalArgumentException("Unexpected base in allele bases " + new String(bases)); throw new IllegalArgumentException("Unexpected base in allele bases \'" + new String(bases)+"\'");
} }
private Allele(String bases, boolean isRef) { private Allele(String bases, boolean isRef) {

4
public/scala/src/org/broadinstitute/sting/queue/engine/QGraph.scala
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@ -138,8 +138,9 @@ class QGraph extends Logging {
validate() validate()
if (running && numMissingValues == 0) { if (running && numMissingValues == 0) {
logger.info("Generating scatter gather jobs.")
val scatterGathers = jobGraph.edgeSet.filter(edge => scatterGatherable(edge)) val scatterGathers = jobGraph.edgeSet.filter(edge => scatterGatherable(edge))
if (!scatterGathers.isEmpty) {
logger.info("Generating scatter gather jobs.")
var addedFunctions = List.empty[QFunction] var addedFunctions = List.empty[QFunction]
for (scatterGather <- scatterGathers) { for (scatterGather <- scatterGathers) {
@ -164,6 +165,7 @@ class QGraph extends Logging {
validate() validate()
} }
} }
}
private def scatterGatherable(edge: QEdge) = { private def scatterGatherable(edge: QEdge) = {
edge match { edge match {

6
public/scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
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@ -286,11 +286,11 @@ object Lsf706JobRunner extends Logging {
// LSB_SHAREDIR/cluster_name/logdir/lsb.acct (man bacct) // LSB_SHAREDIR/cluster_name/logdir/lsb.acct (man bacct)
// LSB_SHAREDIR/cluster_name/logdir/lsb.events (man bhist) // LSB_SHAREDIR/cluster_name/logdir/lsb.events (man bhist)
logger.debug("Job Id %s status / exitStatus / exitInfo: ??? / ??? / ???".format(runner.jobId)) logger.debug("Job Id %s status / exitStatus / exitInfo: ??? / ??? / ???".format(runner.jobId))
val unknownStatusSeconds = (System.currentTimeMillis - runner.lastStatusUpdate) val unknownStatusMillis = (System.currentTimeMillis - runner.lastStatusUpdate)
if (unknownStatusSeconds > (unknownStatusMaxSeconds * 1000L)) { if (unknownStatusMillis > (unknownStatusMaxSeconds * 1000L)) {
// Unknown status has been returned for a while now. // Unknown status has been returned for a while now.
runner.updateStatus(RunnerStatus.FAILED) runner.updateStatus(RunnerStatus.FAILED)
logger.error("Unable to read LSF status for %d minutes: job id %d: %s".format(unknownStatusSeconds/60, runner.jobId, runner.function.description)) logger.error("Unable to read LSF status for %0.2f minutes: job id %d: %s".format(unknownStatusMillis/(60 * 1000D), runner.jobId, runner.function.description))
} }
} }