USeq Source Code

2. SamTranscriptomeParser
a) Attempts to report actual chromsome length uses input file header.
b) If the chromosome length cannot be found in the input file header, the app will report the last observed position in the chromosome (previous bevior). I
c) @RG and @PG lines from input file are maintained
3. AlignmentEndTrimmer:
a) Supports hard-clip cigar tag
b) Incorporated most recent picard API, which cleaned up some sam validation errors
c) Now uses the IH tag to help match pairs when multiple alignments are reported per read.
4) ExportExons
a) Exon are named based on gene strand.