/
io.go
48 lines (39 loc) · 796 Bytes
/
io.go
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package io
import (
"github.com/biogo/hts/bam"
"github.com/biogo/hts/sam"
"os"
)
func ReadBam(file string, cpus int, qualityFilter int, discardSecondary bool) <-chan *sam.Record {
var fi *os.File
var err error
var br *bam.Reader
reads := make(chan *sam.Record, 1000)
if file == "stdin" || file == "-" {
fi = os.Stdin
} else {
fi, err = os.Open(file)
}
if err != nil {
ExitWithMessage(err)
}
br, err = bam.NewReader(fi, cpus)
if err != nil {
ExitWithMessage(err)
}
go func() {
for {
if sr, err3 := br.Read(); err3 != nil {
break
} else {
// If primary alignment, we take it
if (!discardSecondary || sr.Flags&sam.Secondary == 0) && int(sr.MapQ) >= qualityFilter {
reads <- sr
}
}
}
br.Close()
close(reads)
}()
return reads
}