Rework strand-specific inference

[smith-chem-wisc]

Rework strand-specific inference

[acesnik]

There's this cool function in the new samtools-1.6

acesnik@DESKTOP-NTA5PMC:~$  samtools flags

About: Convert between textual and numeric flag representation
Usage: samtools flags INT|STR[,...]

Flags:
        0x1     PAIRED        .. paired-end (or multiple-segment) sequencing technology
        0x2     PROPER_PAIR   .. each segment properly aligned according to the aligner
        0x4     UNMAP         .. segment unmapped
        0x8     MUNMAP        .. next segment in the template unmapped
        0x10    REVERSE       .. SEQ is reverse complemented
        0x20    MREVERSE      .. SEQ of the next segment in the template is reversed
        0x40    READ1         .. the first segment in the template
        0x80    READ2         .. the last segment in the template
        0x100   SECONDARY     .. secondary alignment
        0x200   QCFAIL        .. not passing quality controls
        0x400   DUP           .. PCR or optical duplicate
        0x800   SUPPLEMENTARY .. supplementary alignment

[acesnik]

Done in #58