Adding three minor new features:

+ -L all now walks over all intervals

+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.

+ Error is thrown if the start position on an interval is higher number than the end position.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -161,10 +161,10 @@ public class GenomeAnalysisEngine {
         initializeIntervals();
 
         ShardStrategy shardStrategy = getShardStrategy(my_walker,
-                                                       microScheduler.getReference(),
+                microScheduler.getReference(),
-                                                       intervals,
+                intervals,
-                                                       argCollection.maximumEngineIterations,
+                argCollection.maximumEngineIterations,
-                                                       readsDataSource != null ? readsDataSource.getReadsInfo().getValidationExclusionList() : null);
+                readsDataSource != null ? readsDataSource.getReadsInfo().getValidationExclusionList() : null);
 
         // execute the microscheduler, storing the results
         return microScheduler.execute(my_walker, shardStrategy, argCollection.maximumEngineIterations);
@@ -180,10 +180,15 @@ public class GenomeAnalysisEngine {
             excludeIntervals = GenomeLocSortedSet.createSetFromList(rawExcludeIntervals);
         }
 
+        if (argCollection.intervals != null && argCollection.intervalMerging.check()) {
+            List <GenomeLoc> parsedIntervals = parseIntervalRegion(argCollection.intervals);
+            intervals = (parsedIntervals == null) ? null: GenomeLocSortedSet.createSetFromList(parsedIntervals);
+        }
+        /*
         if (argCollection.intervals != null && argCollection.intervalMerging.check()) {
             intervals = GenomeLocSortedSet.createSetFromList(parseIntervalRegion(argCollection.intervals));
         }
-
+          */
         if ( excludeIntervals != null ) {
             GenomeLocSortedSet toPrune = intervals == null ? GenomeLocSortedSet.createSetFromSequenceDictionary(this.referenceDataSource.getSequenceDictionary()) : intervals;
             long toPruneSize = toPrune.coveredSize();
@@ -342,6 +347,15 @@ public class GenomeAnalysisEngine {
     public static List<GenomeLoc> parseIntervalRegion(final List<String> intervals, IntervalMergingRule mergingRule) {
         List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
         for (String interval : intervals) {
+            // if any interval argument is '-L all', consider all loci by returning no intervals
+            if (interval.equals("all")) {
+                if (intervals.size() != 1) {
+                    // throw error if '-L all' is not only interval - potentially conflicting commands
+                    throw new StingException(String.format("Conflicting arguments: Intervals given along with \"-L all\""));
+                }
+                return new ArrayList<GenomeLoc>();
+            }
+
             if (new File(interval).exists()) {
                 // support for the bed style interval format
                 if (interval.toUpperCase().endsWith(".BED")) {

java/src/org/broadinstitute/sting/utils/GenomeLocParser.java

@@ -190,6 +190,8 @@ public class GenomeLocParser {
         if (contig == null)
             throw new StingException("Invalid Genome Location contig == null : " + str);
 
+        if (start > stop)
+		    throw new StingException("Invalid Genome Location string; start position comes after end position: " + str );
 		        
 		if (!isContigValid(contig))
             throw new StingException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
@@ -226,7 +228,7 @@ public class GenomeLocParser {
             locs = mergeIntervalLocations(locs, rule);            
             return locs;
         } catch (Exception e) { // TODO: fix this so that it passes the message from the exception, and doesn't print it out
-            throw new StingException(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str), e);
+            throw new StingException(String.format("Invalid locations string: %s, format is loc1;loc2; where loc1 < loc2. Each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str), e);
         }                                                                                                                        
     }