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there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@390 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-14 00:45:47 +00:00
parent 8e6093d5a5
commit bc43c0eefc
1 changed files with 10 additions and 4 deletions
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14
java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
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@ -158,6 +158,10 @@ public class PileBuilder implements RecordPileReceiver {
List<MultipleAlignment> piles = doMultipleAlignment2(seqs);
if ( piles.size() > 2 ) {
System.out.println("WARNING: " + piles.size() + " piles appear to be disjoint");
}
// System.out.print("Distance between final piles: "+distance(alignments1, alignments2));
// System.out.print("; diameter of PILE1: "+ diameter(alignments1));
// System.out.println("; diameter of PILE2: "+ diameter(alignments2));
@ -887,16 +891,18 @@ public List<MultipleAlignment> doMultipleAlignment2(IndexedSequence[] seqs) {
}
}
}
// System.out.println("joining pile "+pile_i +" and pile " + pile_j +" on seqs " + best_i +" and " + best_j );
if ( d >= 1e99 ) break; // oops, we could not stitch any of the remaining piles together!
// got the closest pair
piles.get(pile_i).add(piles.get(pile_j),alignments.get(best_i,best_j));
// System.out.println("JOINED PILE: \n"+piles.get(pile_i).toString());
// System.out.println("JOINED PILE: \n"+piles.get(pile_i).toString());
piles.remove(pile_j);
npiles--;
}
alignments1 = piles.get(0);
alignments2 = piles.get(1);
// alignments1 = piles.get(0);
// alignments2 = piles.get(1);
// System.out.println("PILE 1: \n"+piles.get(0).toString());