Fixed bug where reads were not paired if there was an indel at the first position of the second read. This fix results in an overall increased computation time.
Fixed bug where a negative total alignment score would be considered really good.
Fixed bug where the transcript path multiplicity was not accounted for in the probability normalization.
Changes to existing options:
Made the multipath alignment (gamp) format from mpmap the default input. Changed the -u option to instead specify that the input is single-path format (gam).
General improvements:
Decreased the maximum search distance when pairing read. This results in an overall decreased computation time without sacrificing accuracy.
Changed it so that the minimum mapping quality is now used for read-pairs instead of incorrectly assuming independence between the two.
Added a mapping quality and multi-mapping read filter to the fragment length distribution estimation.
Added a scoring difference filter that removes low probable alignment paths with a score that is 24 below the best scoring alignment path. This can be changed using the -w, --filt-score-diff option.
Bug fixes:
Changes to existing options:
-uoption to instead specify that the input is single-path format (gam).General improvements:
-w, --filt-score-diffoption.