Added read name, start, and end fields to pileup. Also, refactored Reads2Ref so that it does not try to create pileups for unmapped reads.
Adding indel realignment transform. Composed of several steps:
- Targets for realignment are generated
- Realignment candidates are generated using Smith-Waterman
- If candidates lead to a sufficient improvement, reads are realigned
Added body of indel realignment code.
Completed indel realignment feature. Now to test and debug.