Verify: Correct read slice coords for negative strand alignments

[Adamtaranto]

May need to have isClipMotif() function check if the current alignment is on the negative strand before extracting sequence for motif search.

Assumptions:

• Align coords are reported in fwd orientation from leftmost ref position.
• CIGAR coords are reported for ref fwd orientation (left to right on ref)
• Read string is not altered from raw read (may be reversed relative to CIGAR coords)

If above are true, then 3' overhang seq for 1000M500S should be retrieved as:

• If forward alignment: Seq[-500:]
• If reverse alignment: Seq[0:500]

and for a 5' alignment 500S1000M:

• If forward alignment: Seq[0:500]
• If reverse alignment: Seq[-500:]

Note: If printing overhang sequence to a summary file we should RC the extracted OH for neg strand alignments.

[Adamtaranto]

Check sam flag for rev status:

# Set Rev flag
$ SAM_FLAG = 16

# Test with hex 0x10 
$ bool(SAM_FLAG & 0x10)

$ TRUE

For other flag codes see flags explained.

[Adamtaranto]

Closing. Non-issue. Turns out both bwa and minimap2 already RC the read when reporting a neg strand alignment.