Track which tile variants each hgvs.Variant appeared in.

[lightning.git] / export.go

diff --git a/export.go b/export.go
index 47ff751afa4f6cc02a317ac1cfa0e34b51e4bb70..38fbeacb5283a96131ea5b4da3fa3216d9f780de 100644 (file)
--- a/export.go
+++ b/export.go
@@ -25,10 +25,15 @@ import (
        log "github.com/sirupsen/logrus"
 )
 
+type tvVariant struct {
+       hgvs.Variant
+       librefs map[tileLibRef]bool
+}
+
 type outputFormat struct {
        Filename string
        Head     func(out io.Writer, cgs []CompactGenome)
-       Print    func(out io.Writer, seqname string, varslice []hgvs.Variant)
+       Print    func(out io.Writer, seqname string, varslice []tvVariant)
        PadLeft  bool
 }
 
@@ -355,7 +360,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
        var outmtx sync.Mutex
        defer outmtx.Lock()
        refpos := 0
-       variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
+       variantAt := map[int][]tvVariant{} // variantAt[chromOffset][genomeIndex*2+phase]
        for refstep, libref := range reftiles {
                select {
                case <-progressbar.C:
@@ -426,10 +431,15 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                                        v.Position += refpos
                                        varslice := variantAt[v.Position]
                                        if varslice == nil {
-                                               varslice = make([]hgvs.Variant, len(cgs)*2)
+                                               varslice = make([]tvVariant, len(cgs)*2)
                                                variantAt[v.Position] = varslice
                                        }
-                                       varslice[cgidx*2+phase] = v
+                                       varslice[cgidx*2+phase].Variant = v
+                                       if varslice[cgidx*2+phase].librefs == nil {
+                                               varslice[cgidx*2+phase].librefs = map[tileLibRef]bool{glibref: true}
+                                       } else {
+                                               varslice[cgidx*2+phase].librefs[glibref] = true
+                                       }
                                }
                        }
                }
@@ -446,7 +456,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                        }
                }
                sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
-               flushvariants := make([][]hgvs.Variant, len(flushpos))
+               flushvariants := make([][]tvVariant, len(flushpos))
                for i, pos := range flushpos {
                        varslice := variantAt[pos]
                        delete(variantAt, pos)
@@ -491,7 +501,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
        }
 }
 
-func bucketVarsliceByRef(varslice []hgvs.Variant) map[string]map[string]int {
+func bucketVarsliceByRef(varslice []tvVariant) map[string]map[string]int {
        byref := map[string]map[string]int{}
        for _, v := range varslice {
                if v.Ref == "" && v.New == "" {
@@ -511,7 +521,7 @@ func headVCF(out io.Writer, cgs []CompactGenome) {
        fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
 }
 
-func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
+func printVCF(out io.Writer, seqname string, varslice []tvVariant) {
        for ref, alts := range bucketVarsliceByRef(varslice) {
                altslice := make([]string, 0, len(alts))
                for alt := range alts {
@@ -539,7 +549,7 @@ func headPVCF(out io.Writer, cgs []CompactGenome) {
        fmt.Fprintf(out, "\n")
 }
 
-func printPVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
+func printPVCF(out io.Writer, seqname string, varslice []tvVariant) {
        for ref, alts := range bucketVarsliceByRef(varslice) {
                altslice := make([]string, 0, len(alts))
                for alt := range alts {
@@ -568,13 +578,13 @@ func printPVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
        }
 }
 
-func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
+func printHGVS(out io.Writer, seqname string, varslice []tvVariant) {
        for i := 0; i < len(varslice)/2; i++ {
                if i > 0 {
                        out.Write([]byte{'\t'})
                }
                var1, var2 := varslice[i*2], varslice[i*2+1]
-               if var1 == var2 {
+               if var1.Variant == var2.Variant {
                        if var1.Ref == var1.New {
                                out.Write([]byte{'.'})
                        } else {
@@ -587,11 +597,11 @@ func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
        out.Write([]byte{'\n'})
 }
 
-func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
+func printHGVSOneHot(out io.Writer, seqname string, varslice []tvVariant) {
        vars := map[hgvs.Variant]bool{}
        for _, v := range varslice {
                if v.Ref != v.New {
-                       vars[v] = true
+                       vars[v.Variant] = true
                }
        }
 
@@ -605,7 +615,7 @@ func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
        for _, v := range sorted {
                fmt.Fprintf(out, "%s.%s", seqname, v.String())
                for i := 0; i < len(varslice); i += 2 {
-                       if varslice[i] == v || varslice[i+1] == v {
+                       if varslice[i].Variant == v || varslice[i+1].Variant == v {
                                out.Write([]byte("\t1"))
                        } else {
                                out.Write([]byte("\t0"))