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This discussion was initially offline. I did the mockup to see if the performance was relatively okay and went from there.
Other libraries are either license incompatible (GATB is Affero GPL); not up to the task (Heng Li's code was raw + zlib only, no bzip2); or not oriented for use as a library (SeqDB as suggested by @luizirber)
To address #641, #355, #77, and #249 I feel that it is time to look for a new C++ FAST[AQ] parser.
A trial of Seqan is ongoing in PR #642
This discussion was initially offline. I did the mockup to see if the performance was relatively okay and went from there.
Other libraries are either license incompatible (GATB is Affero GPL); not up to the task (Heng Li's code was raw + zlib only, no bzip2); or not oriented for use as a library (SeqDB as suggested by @luizirber)
See also: https://www.biostars.org/p/486/
Seqan already supports SAM/BAM, which will be useful for #523
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