Staden Package "io_lib" (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats.
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Fix CRAM QS values where ambiguity codes are in the reference. #52
Commit 0aa2af3 changes QS encoding from verbatim copying out of s->qual_blk and into calling codecs[DS_QS]->encode. This was part of the plan to be able to perform the data transforms on QS, included in CRAM 4.0 prototype.
Unfortunately the ordering was wrong, with a copy of all quals followed by encoding any explicit QS items produced by the feature codes. The correct ordering is the reversal of this.
Commit 0aa2af3 changes QS encoding from verbatim copying out of s->qual_blk and into calling codecs[DS_QS]->encode. This was part of the plan to be able to perform the data transforms on QS, included in CRAM 4.0 prototype.
Unfortunately the ordering was wrong, with a copy of all quals followed by encoding any explicit QS items produced by the feature codes. The correct ordering is the reversal of this.