Call Integration Sites Performance Update

The methods for pairing BLAT aligned data from paired-end sequence reads has been recoded to decrease cpu-time and required memory. The output for unique integration sites (sites that can be uniquely mapped to a genomic location) are identical to v1.0.1, while multihit genomic locations are more fully represented in the output. Further, there is better tracking of chimeric reads. See commit fec1095 for all changes.

Update to Integration Site Calling Methods

Updates to methods which improve performance and accuracy of intSiteCaller, such as modifying the alignment calling methods to better reflect the whole sequence alignments rather than partials (majority of changes accepted on commit acd0014).

intsitescaller

bug fix, reduce by 0

First stable integration site caller

This is the first release of the integration site caller for both unique and multihits by BushmanLab.