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 reverse complemented |
| 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 |