@gmod/cram
Version:
read CRAM files with pure Javascript
51 lines • 1.42 kB
JavaScript
const Constants = {
CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
CRAM_FLAG_DETACHED: 1 << 1,
CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,
CRAM_FLAG_NO_SEQ: 1 << 3,
CRAM_FLAG_MASK: (1 << 4) - 1,
// mate read is reversed
CRAM_M_REVERSE: 1,
// mated read is unmapped
CRAM_M_UNMAP: 2,
// the read is paired in sequencing, no matter whether it is mapped in a pair
BAM_FPAIRED: 1,
// the read is mapped in a proper pair
BAM_FPROPER_PAIR: 2,
// the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
BAM_FUNMAP: 4,
// the mate is unmapped
BAM_FMUNMAP: 8,
// the read is mapped to the reverse strand
BAM_FREVERSE: 16,
// the mate is mapped to the reverse strand
BAM_FMREVERSE: 32,
// this is read1
BAM_FREAD1: 64,
// this is read2
BAM_FREAD2: 128,
// not primary alignment
BAM_FSECONDARY: 256,
// QC failure
BAM_FQCFAIL: 512,
// optical or PCR duplicate
BAM_FDUP: 1024,
// supplementary alignment
BAM_FSUPPLEMENTARY: 2048,
BAM_CMATCH: 0,
BAM_CINS: 1,
BAM_CDEL: 2,
BAM_CREF_SKIP: 3,
BAM_CSOFT_CLIP: 4,
BAM_CHARD_CLIP: 5,
BAM_CPAD: 6,
BAM_CEQUAL: 7,
BAM_CDIFF: 8,
BAM_CBACK: 9,
BAM_CIGAR_STR: 'MIDNSHP:XB',
BAM_CIGAR_SHIFT: 4,
BAM_CIGAR_MASK: 0xf,
BAM_CIGAR_TYPE: 0x3c1a7,
};
export default Constants;
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