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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-09-09 14:41:24 -04:00
parent 36913706c0 8ca205f1a9
commit 3dd0f59765
4 changed files with 16 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java
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@ -137,6 +137,10 @@ public class CommandLineGATK extends CommandLineExecutable {
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
if ( t.getCause() != null && t.getCause().getMessage().contains("No space left on device") )
exitSystemWithUserError(new UserException.NoSpaceOnDevice());
// masked out of memory error
if ( t.getCause() != null && t.getCause() instanceof OutOfMemoryError )
exitSystemWithUserError(new UserException.NotEnoughMemory());
}
/**

8
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
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@ -246,6 +246,14 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
*/
private void addNewOverlappingIntervals(GenomeLoc refLocus) {
GenomeLoc interval = intervalListIterator.peek();
// skip any intervals with no coverage that we have passed
while (interval != null && interval.isBefore(refLocus)) {
intervalListIterator.next(); // discard the interval (we've already added it to the map)
interval = intervalListIterator.peek();
}
// add any intervals that overlap this one
while (interval != null && !interval.isPast(refLocus)) {
intervalMap.put(interval, createIntervalStatistic(interval));
intervalListIterator.next(); // discard the interval (we've already added it to the map)

4
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java
View File

@ -94,8 +94,10 @@ public class ErrorThrowing extends RodWalker<Integer,Integer> implements TreeRed
throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_1);
} else if ( exceptionToThrow.equals("SamError2") ) {
throw new RuntimeException(CommandLineGATK.PICARD_TEXT_SAM_FILE_ERROR_2);
} else if ( exceptionToThrow.equals("NoSpace") ) {
} else if ( exceptionToThrow.equals("NoSpace1") ) {
throw new net.sf.samtools.util.RuntimeIOException(new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)"));
} else if ( exceptionToThrow.equals("NoSpace2") ) {
throw new net.sf.samtools.SAMException("Exception writing BAM index file", new java.io.IOException("No space left on device java.io.FileOutputStream.writeBytes(Native Method)"));
} else {
throw new UserException.BadArgumentValue("exception", "exception isn't a recognized value " + exceptionToThrow);
}

2
public/java/src/org/broadinstitute/sting/utils/help/ForumAPIUtils.java
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@ -44,7 +44,7 @@ public class ForumAPIUtils {
/**
* How we post to the forum
*/
private final static String API_URL = "https://gatk.vanillaforums.com/";
private final static String API_URL = "https://gatkforums.broadinstitute.org/api/v1/";
final private static String ACCESS_TOKEN = "access_token=";
public static List<String> getPostedTools(String forumKey) {