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https://github.com/metabarcoding/obitools4.git
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154 lines
3.5 KiB
Go
154 lines
3.5 KiB
Go
package obiformats
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// #cgo CFLAGS: -g -Wall
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// #cgo LDFLAGS: -lz
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// #include <stdlib.h>
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// #include "fastseq_read.h"
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import "C"
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import (
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"fmt"
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"os"
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"unsafe"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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)
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func _FastseqReader(seqfile C.fast_kseq_p,
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iterator obiiter.IBioSequenceBatch,
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batch_size int) {
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var comment string
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i := 0
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ii := 0
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slice := obiseq.MakeBioSequenceSlice()
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for l := int64(C.next_fast_sek(seqfile)); l > 0; l = int64(C.next_fast_sek(seqfile)) {
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s := seqfile.seq
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csequence := cutils.ByteSlice(unsafe.Pointer(s.seq.s), int(s.seq.l))
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sequence := obiseq.GetSlice()
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sequence = append(sequence, csequence...)
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//sequence := C.GoBytes(unsafe.Pointer(s.seq.s),
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// C.int(s.seq.l))
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name := C.GoString(s.name.s)
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if s.comment.l > C.ulong(0) {
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comment = C.GoString(s.comment.s)
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} else {
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comment = ""
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}
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rep := obiseq.NewBioSequence(name, sequence, comment)
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if s.qual.l > C.ulong(0) {
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cquality := cutils.ByteSlice(unsafe.Pointer(s.qual.s), int(s.qual.l))
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l := int(s.qual.l)
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quality := obiseq.GetSlice()
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shift := uint8(seqfile.shift)
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for j := 0; j < l; j++ {
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quality = append(quality, uint8(cquality[j])-shift)
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}
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rep.SetQualities(quality)
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}
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slice = append(slice, rep)
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ii++
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if ii >= batch_size {
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//log.Printf("\n==> Pushing sequence batch\n")
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// start := time.Now()
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iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
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// elapsed := time.Since(start)
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// log.Printf("\n==>sequences pushed after %s\n", elapsed)
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slice = obiseq.MakeBioSequenceSlice()
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i++
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ii = 0
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}
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}
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if len(slice) > 0 {
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iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
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}
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iterator.Done()
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}
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func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.IBioSequenceBatch, error) {
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opt := MakeOptions(options)
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name := C.CString(filename)
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defer C.free(unsafe.Pointer(name))
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pointer := C.open_fast_sek_file(name, C.int32_t(opt.QualityShift()))
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var err error
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err = nil
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if pointer == nil {
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err = fmt.Errorf("cannot open file %s", filename)
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return obiiter.NilIBioSequenceBatch, err
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}
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size := int64(-1)
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fi, err := os.Stat(filename)
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if err == nil {
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size = fi.Size()
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log.Debugf("File size of %s is %d bytes\n", filename, size)
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} else {
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size = -1
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}
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newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
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newIter.Add(1)
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go func() {
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newIter.WaitAndClose()
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log.Debugln("End of the fastq file reading")
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}()
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log.Debugln("Start of the fastq file reading")
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go _FastseqReader(pointer, newIter, opt.BatchSize())
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parser := opt.ParseFastSeqHeader()
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if parser != nil {
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return IParseFastSeqHeaderBatch(newIter, options...), err
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}
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return newIter, err
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}
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func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
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ib, err := ReadFastSeqBatchFromFile(filename, options...)
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return ib.SortBatches().IBioSequence(), err
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}
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func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch {
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opt := MakeOptions(options)
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newIter := obiiter.MakeIBioSequenceBatch(opt.BufferSize())
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newIter.Add(1)
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go func() {
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newIter.WaitAndClose()
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}()
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go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
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newIter, opt.BatchSize())
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return newIter
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}
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func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
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ib := ReadFastSeqBatchFromStdin(options...)
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return ib.SortBatches().IBioSequence()
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}
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