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// Copyright ©2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package sam
// A Flags represents a BAM record's alignment FLAG field.
type Flags uint16
const (
Paired Flags = 1 << iota // The read is paired in sequencing, no matter whether it is mapped in a pair.
ProperPair // The read is mapped in a proper pair.
Unmapped // The read itself is unmapped; conflictive with ProperPair.
MateUnmapped // The mate is unmapped.
Reverse // The read is mapped to the reverse strand.
MateReverse // The mate is mapped to the reverse strand.
Read1 // This is read1.
Read2 // This is read2.
Secondary // Not primary alignment.
QCFail // QC failure.
Duplicate // Optical or PCR duplicate.
Supplementary // Supplementary alignment, indicates alignment is part of a chimeric alignment.
)
// String representation of BAM alignment flags:
// 0x001 - p - Paired
// 0x002 - P - ProperPair
// 0x004 - u - Unmapped
// 0x008 - U - MateUnmapped
// 0x010 - r - Reverse
// 0x020 - R - MateReverse
// 0x040 - 1 - Read1
// 0x080 - 2 - Read2
// 0x100 - s - Secondary
// 0x200 - f - QCFail
// 0x400 - d - Duplicate
// 0x800 - S - Supplementary
//
// Note that flag bits are represented high order to the right.
func (f Flags) String() string {
// If 0x01 is unset, no assumptions can be made about 0x02, 0x08, 0x20, 0x40 and 0x80
const pairedMask = ProperPair | MateUnmapped | MateReverse | MateReverse | Read1 | Read2
if f&1 == 0 {
f &^= pairedMask
}
const flags = "pPuUrR12sfdS"
b := make([]byte, len(flags))
for i, c := range flags {
if f&(1<<uint(i)) != 0 {
b[i] = byte(c)
} else {
b[i] = '-'
}
}
return string(b)
}
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