Enum
BamFlags
Shortcuts to the bitmask flags for BAM/SAM files.
BamFlags
Include Headers
seqan/bam_io.h
Remarks
Also see the SAM standard on these flags for more explanation.
Values
BAM_FLAG_MULTIPLE
0x0001 Template has multiple fragments in sequencing.
BAM_FLAG_ALL_PROPER
0x0002 All fragments have been aligned properly.
BAM_FLAG_UNMAPPED
0x0004 This fragment could not be mapped.
BAM_FLAG_NEXT_UNMAPPED
0x0008 Next fragment is unmapped.
BAM_FLAG_RC
0x0010 This fragment is reverse-complemented.
BAM_FLAG_NEXT_RC
0x0020 Next fragment is reverse-complemented.
BAM_FLAG_FIRST
0x0040 This fragment is the first one in its template.
BAM_FLAG_LAST
0x0080 This fragment is the last one in its template.
BAM_FLAG_SECONDARY
0x0100 This is a secondary alignment.
BAM_FLAG_QC_NO_PASS
0x0200 Does not pass quality controls.
BAM_FLAG_DUPLICATE
0x0400 PCR or optical duplicate.
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