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move warning about strictly adjacent intervals in a contig from 'remap' to 'read', so it is issued only once 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1218 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-07-10 17:58:11 +00:00
parent aa4f60d980
commit 1401606344
1 changed files with 12 additions and 10 deletions
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22
java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
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@ -146,7 +146,13 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
while ( p2 < line.length() && line.charAt(p2) != ',') p2++; // next comma or end-of-line
while ( p2 != p1 ) {
segments.add(GenomeLocParser.parseGenomeLoc(line.substring(p1, p2)));
GenomeLoc newSegment = GenomeLocParser.parseGenomeLoc(line.substring(p1, p2));
if ( segments.size() > 0 &&
segments.get(segments.size()-1).getStop()+1 == newSegment.getStart() &&
segments.get(segments.size()-1).getContigIndex() == newSegment.getContigIndex())
System.out.println("WARNING: strictly adjacent segments found in custom contig "+name);
segments.add(newSegment);
p1 = p2+1; // set p1 after the comma
while ( p1 < line.length() && Character.isWhitespace(line.charAt(p1))) p1++; // skip whitespaces
@ -183,8 +189,8 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
}
}
/** Remaps a record (read) aligned to a custom contig back onto the master reference, using the
* mapping of that custom contig to the master reference. If the map does not have mapping information for
/** Remaps a record (read) aligned to a custom contig back onto the master reference.
* If the map does not have mapping information for
* the contig, an exception will be thrown. This method changes read's reference name, start position and
* cigar, as well as the read's file header (must be provided).
*
@ -276,8 +282,6 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
if ( refPos < currStop + 1 )
throw new StingException("Contig "+oldRefName+" has segments that are out of order or strictly adjacent: currently unsupported");
if ( refPos == currStop + 1 )
System.out.println("WARNING: Contig "+oldRefName+" has segments that are strictly adjacent");
// add "deletion" w/respect to the master ref over the region between adjacent segments:
deletionLength += (int)(refPos-currStop-1);
@ -327,11 +331,9 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
if ( refPos < currStop + 1 )
throw new StingException("Contig "+oldRefName+
" has segments that are out of order or strictly adjacent: currently unsupported");
if ( refPos == currStop + 1 ) {
System.out.println("WARNING: Contig "+oldRefName+
" has segments that are strictly adjacent");
} else {
// add "deletion" w/respect to the master ref over the region between adjacent segments:
if ( refPos > currStop + 1 ) {
// add "deletion" w/respect to the master ref over the region between adjacent segments
// (and do not add anything if segments are strictly adjacent, i.e. refPos == currStop+1):
newCigar.add(new CigarElement((int)(refPos-currStop-1),CigarOperator.D));
}
currStop = gl.getStop();