vadimzalunin/crammer — Issue #12: Incorrectly restored cigar causes alignment discrepancies
Author: vadimzalunin
Created: 2012-02-08 11:29:54+00:00
State: open

Examples:
3S2I45M vs 5S45M
30M1D592N2D20M vs 30M595D
18M2D702N1D32M vs 18M705D
9M2D398N1D41M vs 9M401D
4S3I43M vs 7S43M
5S1I6M3177N38M vs 6S6M3177D38M
22M2899N22M1I5S vs 22M2899D22M6S
22M2899N22M1I5S vs 22M2899D22M6S
31M1D2420N1D19M vs 31M2422D
22M1D118N1D28M vs 22M120D

Given the same alignment start the reads still have the following problems:
alignment end
unclipped alignment start
unclipped alignment end