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

Complete the switch statement to deal with all possible cigar operators for Kris. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-05-05 13:41:05 +00:00
parent f75e54e3f7
commit 64640d6b17
1 changed files with 4 additions and 33 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

37
java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
View File

@ -108,6 +108,9 @@ public class AlignmentUtils {
case N:
refIndex += ce.getLength();
break;
case H:
case P:
break;
default: throw new StingException("The " + ce.getOperator() + " cigar element is not currently supported");
}
@ -226,44 +229,12 @@ public class AlignmentUtils {
return n;
}
public static String toString(Cigar cig) {
StringBuilder b = new StringBuilder();
for ( int i = 0 ; i < cig.numCigarElements() ; i++ ) {
char c='?';
switch ( cig.getCigarElement(i).getOperator() ) {
case M : c = 'M'; break;
case D : c = 'D'; break;
case I : c = 'I'; break;
}
b.append(cig.getCigarElement(i).getLength());
b.append(c);
}
return b.toString();
}
public static String alignmentToString(final Cigar cigar,final String seq, final String ref, final int posOnRef ) {
return alignmentToString( cigar, seq, ref, posOnRef, 0 );
}
public static String cigarToString(Cigar cig) {
if ( cig == null )
return "null";
StringBuilder b = new StringBuilder();
for ( int i = 0 ; i < cig.numCigarElements() ; i++ ) {
char c='?';
switch ( cig.getCigarElement(i).getOperator() ) {
case M : c = 'M'; break;
case D : c = 'D'; break;
case I : c = 'I'; break;
}
b.append(cig.getCigarElement(i).getLength());
b.append(c);
}
return b.toString();
return cig.toString();
}
public static String alignmentToString(final Cigar cigar,final String seq, final String ref, final int posOnRef, final int posOnRead ) {