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Added detection of interval files with zero length to the GATK, and removed it from the interval merger walker: this was a critical blocking emergency issue for Eric. 

also fixed some verbage in the GAEngine.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1449 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-08-21 05:35:49 +00:00
parent 0bdecd8651
commit cd711d7697
3 changed files with 8 additions and 13 deletions
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4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -103,12 +103,12 @@ public class GenomeAnalysisEngine {
public Object execute(GATKArgumentCollection args, Walker<?,?> my_walker) {
// validate our parameters
if (args == null) {
throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can be null.");
throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
}
// validate our parameters
if (my_walker == null)
throw new StingException("The walker passed to GenomeAnalysisEngine can be null.");
throw new StingException("The walker passed to GenomeAnalysisEngine can not be null.");
// save our argument parameter
this.argCollection = args;

9
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
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@ -114,15 +114,6 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
* @return a linked list of sorted, merged intervals.
*/
private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
// ignore zero-length intervals files.
for (int i = 0; i < intervalsSource.size(); i++)
{
File f = new File(intervalsSource.get(i));
long size = f.length();
if (size == 0) { intervalsSource.remove(i); }
}
List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet();
for ( GenomeLoc parsedInterval : parsedIntervals )

8
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -321,8 +321,12 @@ public class GenomeLocParser {
*/
List<GenomeLoc> ret = null;
try {
IntervalList il = IntervalList.fromFile(new File(file_name));
File inputFile = new File(file_name);
// sometimes we see an empty file passed as a parameter, if so return an empty list
if (inputFile.length() < 1) return new ArrayList<GenomeLoc>();
IntervalList il = IntervalList.fromFile(inputFile);
// iterate through the list of merged intervals and add then as GenomeLocs
ret = new ArrayList<GenomeLoc>();
for (Interval interval : il.getUniqueIntervals()) {