From 908a66b02cdf030b2339d11ad89d8c09647a1b54 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Thu, 2 Dec 2021 13:39:36 -0500 Subject: [PATCH] Add null csv rows for ref/undiffed. Ensure 0 means ref in matrix. refs #18496 Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- hgvs/diff.go | 4 +++ slicenumpy.go | 82 ++++++++++++++++++++++++++++++++++++++------------- 2 files changed, 65 insertions(+), 21 deletions(-) diff --git a/hgvs/diff.go b/hgvs/diff.go index e25e13b920..12fa7c77c4 100644 --- a/hgvs/diff.go +++ b/hgvs/diff.go @@ -23,6 +23,10 @@ func (v *Variant) String() string { switch { case len(v.New) == 0 && len(v.Ref) == 0: return fmt.Sprintf("%d=", v.Position) + case len(v.New) == 1 && v.New == v.Ref: + return fmt.Sprintf("%d=", v.Position) + case v.New == v.Ref: + return fmt.Sprintf("%d_%d=", v.Position, v.Position+len(v.Ref)-1) case len(v.New) == 0 && len(v.Ref) == 1: return fmt.Sprintf("%ddel", v.Position) case len(v.New) == 0: diff --git a/slicenumpy.go b/slicenumpy.go index 9353488cac..24904155c5 100644 --- a/slicenumpy.go +++ b/slicenumpy.go @@ -308,6 +308,12 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s go func() { defer throttleCPU.Release() count := make(map[[blake2b.Size256]byte]int, len(variants)) + + rt := reftile[tag] + if rt != nil { + count[blake2b.Sum256(rt.tiledata)] = 0 + } + for _, cg := range cgs { idx := int(tag-tagstart) * 2 if idx < len(cg.Variants) { @@ -349,6 +355,9 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s remap[i] = rank[tv.Blake2b] } variantRemap[tag-tagstart] = remap + if rt != nil { + rt.variant = rank[blake2b.Sum256(rt.tiledata)] + } }() } throttleCPU.Wait() @@ -374,19 +383,20 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s // mention it in annotations?) continue } + fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos) variants := seq[tag] reftilestr := strings.ToUpper(string(rt.tiledata)) remap := variantRemap[tag-tagstart] done := make([]bool, len(variants)) for v, tv := range variants { v := remap[v] - if done[v] { + if v == rt.variant || done[v] { continue } else { done[v] = true } if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) { - fmt.Fprintf(annow, "%d,%d,%d,.,%s,%d,.,,\n", tag, outcol, v, rt.seqname, rt.pos) + fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos) continue } if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 { @@ -467,7 +477,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s cols += len(chunk) / rows } out := make([]int16, rows*cols) - hgvs := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase) + hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase) startcol := 0 for outIdx, chunk := range toMerge { chunkcols := len(chunk) / rows @@ -490,13 +500,23 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s if len(line) == 0 { continue } - fields := bytes.SplitN(line, []byte{','}, 8) + fields := bytes.SplitN(line, []byte{','}, 9) + tag, _ := strconv.Atoi(string(fields[0])) incol, _ := strconv.Atoi(string(fields[1])) tileVariant, _ := strconv.Atoi(string(fields[2])) hgvsID := string(fields[3]) seqname := string(fields[4]) pos, _ := strconv.Atoi(string(fields[5])) refseq := fields[6] + if hgvsID == "" { + // Null entry for un-diffable + // tile variant + continue + } + if hgvsID == "=" { + // Null entry for ref tile + continue + } if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) { // The tile intersects one of // the selected regions, but @@ -504,24 +524,44 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s // variant does not. continue } - fmt.Fprintf(annow, "%s,%d,%d,%s,%s,%d,%s,%s\n", fields[0], incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7]) - hgvscols := hgvs[hgvsID] - if hgvscols[0] == nil { - hgvscols = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))} - hgvs[hgvsID] = hgvscols + hgvsColPair := hgvsCols[hgvsID] + if hgvsColPair[0] == nil { + // values in new columns start + // out as -1 ("no data yet") + // or 0 ("=ref") here, may + // change to 1 ("hgvs variant + // present") below, either on + // this line or a future line. + hgvsColPair = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))} + rt, ok := reftile[tagID(tag)] + if !ok { + err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag) + return 1 + } + for ph := 0; ph < 2; ph++ { + for row := 0; row < rows; row++ { + v := chunk[row*chunkcols+incol*2+ph] + if tileVariantID(v) == rt.variant { + hgvsColPair[ph][row] = 0 + } else { + hgvsColPair[ph][row] = -1 + } + } + } + hgvsCols[hgvsID] = hgvsColPair + hgvsref := hgvs.Variant{ + Position: pos, + Ref: string(refseq), + New: string(refseq), + } + fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, rt.variant, seqname, hgvsref.String(), seqname, pos, refseq, refseq, fields[8]) } + fmt.Fprintf(annow, "%d,%d,%d,%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7], fields[8]) for ph := 0; ph < 2; ph++ { for row := 0; row < rows; row++ { v := chunk[row*chunkcols+incol*2+ph] if int(v) == tileVariant { - if len(hgvsID) == 0 { - // we have the tile variant sequence, but the diff against ref didn't work out (see lendiff above) - hgvscols[ph][row] = -2 - } else { - hgvscols[ph][row] = 1 - } - } else if v < 0 { - hgvscols[ph][row] = -1 + hgvsColPair[ph][row] = 1 } } } @@ -543,11 +583,11 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s } out = nil - cols = len(hgvs) * 2 + cols = len(hgvsCols) * 2 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols) out = make([]int16, rows*cols) - hgvsIDs := make([]string, 0, len(hgvs)) - for hgvsID := range hgvs { + hgvsIDs := make([]string, 0, len(hgvsCols)) + for hgvsID := range hgvsCols { hgvsIDs = append(hgvsIDs, hgvsID) } sort.Strings(hgvsIDs) @@ -555,7 +595,7 @@ func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, s for idx, hgvsID := range hgvsIDs { fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID) for ph := 0; ph < 2; ph++ { - hgvscol := hgvs[hgvsID][ph] + hgvscol := hgvsCols[hgvsID][ph] for row, val := range hgvscol { out[row*cols+idx*2+ph] = val } -- 2.30.2