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0.0.3-beta add --fast, fix go-collection usage
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,152 @@ | ||
| package main | ||
|
|
||
| import ( | ||
| "github.com/biogo/hts/sam" | ||
| "github.com/golang-collections/collections/set" | ||
| "strings" | ||
| "sync" | ||
| ) | ||
|
|
||
| func workerFast( | ||
| wg *sync.WaitGroup, refs chan *ChanChunk, w chan string, | ||
| omopolymericPositions, splicePositions, targetPositions map[string]*set.Set, | ||
| chrRefs map[string][]byte) { | ||
| defer wg.Done() | ||
|
|
||
| for { | ||
| ref, ok := <-refs | ||
| if !ok { | ||
| break | ||
| } | ||
|
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| //chrRef, err := fetchFasta(ref.ToRegion()) | ||
| //if err != nil { | ||
| // sugar.Warnf("try to modify %s", ref) | ||
| // chrRef, err = fetchFasta(ref.SwitchRegion()) | ||
| //} | ||
| //if err != nil { | ||
| // sugar.Fatal(err) | ||
| //} | ||
|
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||
| chrRef, ok := chrRefs[ref.Ref] | ||
| if !ok { | ||
| sugar.Errorf("failed to get %s from reference", ref.Ref) | ||
| continue | ||
| } | ||
|
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||
| iter, err := fetchBamFast(ref.Chunks) | ||
| if err != nil { | ||
| sugar.Fatal(err) | ||
| } | ||
|
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||
| lastEnd := 0 | ||
| total := 0 | ||
| edits := make(map[int]*EditsInfo) | ||
| for iter.Next() { | ||
| record := NewRecord(iter.Record()) | ||
|
|
||
| if lastEnd == 0 { | ||
| lastEnd = record.End | ||
| } | ||
|
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| total++ | ||
|
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| if !filterReads(record) { | ||
| continue | ||
| } | ||
|
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||
| start, index := 0, 0 | ||
| for _, i := range record.Cigar { | ||
| if i.Type() == sam.CigarMatch { | ||
| for j := 1; j <= i.Len(); j++ { | ||
| at := index + j - 1 | ||
|
|
||
| if at >= record.Seq.Length { | ||
| sugar.Errorf("%s - %d - %d - %d", record.Cigar, index, at, record.Seq.Length) | ||
| sugar.Fatal(record.SeqString()) | ||
| } | ||
|
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| genomic := start + record.Start | ||
|
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| if _, ok := edits[genomic]; !ok { | ||
| edits[genomic] = NewEditsInfo(ref.Ref, chrRef[genomic-1], genomic) | ||
| } | ||
|
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||
| edits[genomic].AddReads(record, at) | ||
| start++ | ||
| } | ||
| index += i.Len() | ||
| } else if i.Type() != sam.CigarDeletion || i.Type() != sam.CigarHardClipped || i.Type() != sam.CigarInsertion { | ||
| start += i.Len() | ||
| } | ||
| } | ||
|
|
||
| if record.Start > lastEnd { | ||
| getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w) | ||
|
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| edits = make(map[int]*EditsInfo) | ||
| lastEnd = record.End | ||
| } | ||
| } | ||
|
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| getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w) | ||
| } | ||
|
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| w <- "done" | ||
| } | ||
|
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||
| func fastMode( | ||
| wg *sync.WaitGroup, w chan string, | ||
| omopolymericPositions, spicePositions, targetPositions map[string]*set.Set) { | ||
| var lock sync.Mutex | ||
| refs := make(chan *ChanChunk) | ||
|
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| references, err := fetchBamRefsFast() | ||
| if err != nil { | ||
| sugar.Fatal(err) | ||
| } | ||
|
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||
| sugar.Infof("load reference from %s", conf.Reference) | ||
| chrRefs := make(map[string][]byte) | ||
| for ref, _ := range references { | ||
| wg.Add(1) | ||
| go func(ref string, wg *sync.WaitGroup, lock *sync.Mutex) { | ||
| defer wg.Done() | ||
| temp, err := fetchFasta(&Region{Chrom: ref}) | ||
| if err != nil { | ||
| sugar.Warnf("try to modify %s", ref) | ||
| if strings.HasPrefix(ref, "chr") { | ||
| temp, err = fetchFasta(&Region{Chrom: strings.ReplaceAll(ref, "chr", "")}) | ||
| } else { | ||
| temp, err = fetchFasta(&Region{Chrom: "chr" + ref}) | ||
| } | ||
| } | ||
| if err != nil { | ||
| sugar.Fatal(err) | ||
| } | ||
| lock.Lock() | ||
| chrRefs[ref] = temp | ||
| lock.Unlock() | ||
| }(ref, wg, &lock) | ||
| } | ||
|
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| wg.Wait() | ||
|
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| wg.Add(1) | ||
| go writer(w, wg) | ||
|
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| for i := 0; i < conf.Process; i++ { | ||
| go workerFast(wg, refs, w, omopolymericPositions, spicePositions, targetPositions, chrRefs) | ||
| wg.Add(1) | ||
| } | ||
|
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| for ref, chunks := range references { | ||
| sugar.Infof("read reads from %s", ref) | ||
| for _, c := range chunks { | ||
| sugar.Debug(c) | ||
| refs <- c | ||
| } | ||
| } | ||
|
|
||
| close(refs) | ||
| } |
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