Direct BAM format output #27
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…rming sam structures and writing into stringstreams. Also using bgzf for reading input.
… format as vectors of uint32_t combining count and operation
…at as vectors of uint32_t combining count and operation without ever storing them in strings
…r values from HTSlib, which are signed 8 bit integers. The traceback then defaults to -1. The parts needed from sam.h are rewritten in a new header abismal_cigar_utils.hpp
…nto bam-format-output
…ith cigar strings in the uint32_t format. This is in place of having to directly include sam.h and use the macros there
…abismal_a_SOURCES. Not sure this is the best place for them.
…re and go through bgzf of htslib
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Slight change to functionality: abismal can now output BAM format directly, without a pipe through samtools view. This introduces a dependence on HTSlib, but has other advantages. The FASTQ input files will be able to be decompressed using threads if needed, and cigar are now built directly without first creating intermediate "expanded" cigar strings.