zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

few more detailed debug printouts conditioned on if (DEBUG), so no real changes... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1214 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-07-10 16:36:57 +00:00
parent 08c4fb86e3
commit a1eb128377
1 changed files with 6 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/gatk/refdata/RODIterator.java
View File

@ -53,23 +53,28 @@ public class RODIterator<ROD extends ReferenceOrderedDatum> implements Iterator<
if ( current != null && current.getLocation().containsP(loc) ) if ( current != null && current.getLocation().containsP(loc) )
return current; return current;
if ( DEBUG ) System.out.printf(" *** starting seek to %s %d%n", loc.getContig(), loc.getStart()); if ( DEBUG ) System.out.printf(" *** starting seek to %s %d (contig %d) from current location %s %d%n", loc.getContig(), loc.getStart(),
loc.getContigIndex(),current==null?"null":current.getLocation().getContig(), current==null?-1:current.getLocation().getStart());
while ( hasNext() ) { while ( hasNext() ) {
ROD proposed = next(); ROD proposed = next();
if( proposed == null ) if( proposed == null )
continue; continue;
//System.out.printf(" -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart()); //System.out.printf(" -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart());
if ( DEBUG ) System.out.println(" proposed at "+proposed.getLocation()+"; contig index="+proposed.getLocation().getContigIndex());
boolean containedP = proposed.getLocation().containsP(loc); boolean containedP = proposed.getLocation().containsP(loc);
//System.out.printf(" %s -> Seeking to %s, at %s => contains = %b%n", current.getName(), loc, current.getLocation(), containedP); //System.out.printf(" %s -> Seeking to %s, at %s => contains = %b%n", current.getName(), loc, current.getLocation(), containedP);
int cmp = proposed.getLocation().compareTo(loc); int cmp = proposed.getLocation().compareTo(loc);
if ( cmp < 0 ) { if ( cmp < 0 ) {
if ( DEBUG ) System.out.println(" we are before...");
// current occurs before loc, continue searching // current occurs before loc, continue searching
continue; continue;
} }
else if ( cmp == 0 || containedP ) { else if ( cmp == 0 || containedP ) {
if ( DEBUG ) System.out.println(" we found overlap...");
result = proposed; result = proposed;
break; break;
} else { } else {
if ( DEBUG ) System.out.println(" we are after...");
// current is after loc // current is after loc
it.pushback(proposed); it.pushback(proposed);
break; break;