* @return string representing read with gaps, clipping etc applied
*/
public String parseCigarToSequence(SAMRecord rec,
* @return string representing read with gaps, clipping etc applied
*/
public String parseCigarToSequence(SAMRecord rec,
- SortedMap<Integer, Integer> insertions, int alignmentStart)
+ SortedMap<Integer, Integer> insertions, int alignmentStart,
+ SequenceI seq)
{
StringBuilder newRead = new StringBuilder();
Iterator<CigarElement> it = rec.getCigar().getCigarElements()
{
StringBuilder newRead = new StringBuilder();
Iterator<CigarElement> it = rec.getCigar().getCigarElements()
- String nextSegment = applyCigarOp(el, next, rec, iit, override);
+ String nextSegment = applyCigarOp(el, next, rec, iit, override, seq);
* an optional <insertion position, length> which can override a
* <position,length> in it to change the length. Set to null if not
* used.
* an optional <insertion position, length> which can override a
* <position,length> in it to change the length. Set to null if not
* used.
* @return
*/
private String applyCigarOp(CigarElement el, int next,
SAMRecord rec, Iterator<Map.Entry<Integer, Integer>> it,
* @return
*/
private String applyCigarOp(CigarElement el, int next,
SAMRecord rec, Iterator<Map.Entry<Integer, Integer>> it,
case EQ:
// matched or mismatched residues
newRead = applyCigarConsumeReadAndRef(next, length, rec, it,
case EQ:
// matched or mismatched residues
newRead = applyCigarConsumeReadAndRef(next, length, rec, it,
// the reference sequence and other reads should have been gapped for
// this insertion, so just add in the residues
newRead.append(read.substring(nextPos, nextPos + length));
// the reference sequence and other reads should have been gapped for
// this insertion, so just add in the residues
newRead.append(read.substring(nextPos, nextPos + length));
* @return
*/
private StringBuilder applyCigarConsumeReadAndRef(int next, int length,
SAMRecord rec, Iterator<Map.Entry<Integer, Integer>> it,
* @return
*/
private StringBuilder applyCigarConsumeReadAndRef(int next, int length,
SAMRecord rec, Iterator<Map.Entry<Integer, Integer>> it,