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fixed another bug in gapped alignment computation 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@185 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-03-25 08:33:57 +00:00
parent 40f45c2333
commit 71d3e8e99b
1 changed files with 11 additions and 2 deletions
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13
java/src/org/broadinstitute/sting/playground/indels/SWPairwiseAlignment.java
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@ -160,6 +160,7 @@ public class SWPairwiseAlignment {
case DSTATE: o = CigarOperator.D; break; case DSTATE: o = CigarOperator.D; break;
} }
segment_length+=p.second;
CigarElement e = new CigarElement(segment_length,o); CigarElement e = new CigarElement(segment_length,o);
lce.add(e); lce.add(e);
Collections.reverse(lce); Collections.reverse(lce);
@ -267,6 +268,7 @@ public class SWPairwiseAlignment {
case ISTATE: o = CigarOperator.I; break; case ISTATE: o = CigarOperator.I; break;
case DSTATE: o = CigarOperator.D; break; case DSTATE: o = CigarOperator.D; break;
} }
segment_length+=p.second;
CigarElement e = new CigarElement(segment_length,o); CigarElement e = new CigarElement(segment_length,o);
lce.add(e); lce.add(e);
Collections.reverse(lce); Collections.reverse(lce);
@ -417,6 +419,7 @@ public void align3(String a, String b) {
case ISTATE: o = CigarOperator.I; break; case ISTATE: o = CigarOperator.I; break;
case DSTATE: o = CigarOperator.D; break; case DSTATE: o = CigarOperator.D; break;
} }
segment_length+=p.second;
CigarElement e = new CigarElement(segment_length,o); CigarElement e = new CigarElement(segment_length,o);
lce.add(e); lce.add(e);
Collections.reverse(lce); Collections.reverse(lce);
@ -555,6 +558,7 @@ public void align3(String a, String b) {
case ISTATE: o = CigarOperator.I; break; case ISTATE: o = CigarOperator.I; break;
case DSTATE: o = CigarOperator.D; break; case DSTATE: o = CigarOperator.D; break;
} }
segment_length+=p.second;
CigarElement e = new CigarElement(segment_length,o); CigarElement e = new CigarElement(segment_length,o);
lce.add(e); lce.add(e);
Collections.reverse(lce); Collections.reverse(lce);
@ -754,8 +758,13 @@ public void align3(String a, String b) {
s2 = "AGACAGAGAAGG"; s2 = "AGACAGAGAAGG";
testMe(s1,s2); testMe(s1,s2);
*/ */
String s1 = "CCAGCACACAGGTATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA"; // String s1 = "CCAGCACACAGGTATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
String s2 = "CCAGCACACATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA"; // String s2 = "CCAGCACACATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTTTTTGA";
// String s1 = "CCCATCTGTCTCCAATCTGCTGTTTTCCAAAAATTAGGGAACTTCAGTTTTCCCTTTGATACTCTGTATTTCTACCAACCACAACGCCAGGGCTGTCCTGCTTCTACAAGTGACAATGACAAATATAGGCCTGAAGGAAGATG";
// String s2 = "AAAATCTGTTTCCAATCTACTGTTTTCCAAAAATTAGGGAAGTTCAGTTTTCCCTTTGATACTCTGTTTCTACCAATCC";
String s1 = "CCCATCTGTCTCCAATCTGCTGTTTTCCAAAAATTAGGGAACTTCAGTTTTCCCTTTGATACTCTGTATTTCTACCAACCACAACGCCAGGGCTGTCCTGCTTCTACAAGTGACAATGACAAATATAGGCCTGAAGGAAGATG";
String s2 = "AAAATCTGTCTCCAATCTACTGTTTTCCAAAAATTAGGGAAGTTCAGTTTTCCCTTTGATACTCTGTTTCTACCAATCC";
testMe(s1,s2); testMe(s1,s2);
} }