Fix coverage score.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/export.go b/export.go
index 42ff4962ad74df0b7729128ea14429e81d25730f..739f8efa1295d6c06176f3f3ebfe9c7cf0ccad77 100644 (file)
--- a/export.go
+++ b/export.go
@@ -321,7 +321,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
        variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
        for refstep, libref := range reftiles {
                reftile := tileVariant[libref]
-               coverage := int64(0) // number of ref bases that are called in genomes -- max is len(reftile.Sequence)*len(cgs)*2
+               tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
                for cgidx, cg := range cgs {
                        for phase := 0; phase < 2; phase++ {
                                if len(cg.Variants) <= int(libref.Tag)*2+phase {
@@ -331,6 +331,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                                if variant == 0 {
                                        continue
                                }
+                               tagcoverage++
                                genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
                                if variant == libref.Variant {
                                        continue
@@ -362,7 +363,6 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                                        }
                                        varslice[cgidx*2+phase] = v
                                }
-                               coverage += int64(len(reftile.Sequence))
                        }
                }
                refpos += len(reftile.Sequence) - taglen
@@ -400,7 +400,7 @@ func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string,
                        }
                        thickend := refpos
                        // coverage score, 0 to 1000
-                       score := 1000 * coverage / int64(len(reftile.Sequence)) / int64(len(cgs)) / 2
+                       score := 1000 * tagcoverage / len(cgs) / 2
                        fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
                                seqname, tilestart, tileend,
                                libref.Tag,

diff --git a/pipeline_test.go b/pipeline_test.go
index 44440962a9ab549111bfdeedb64c5b4e2f054ced..4dd544d81388a8975c33e8ed781aa234f14c2c52 100644 (file)
--- a/pipeline_test.go
+++ b/pipeline_test.go
@@ -126,12 +126,12 @@ chr2      471     GG      AA      0/1     0/0
        c.Check(err, check.IsNil)
        c.Logf("%s", string(bedout))
        c.Check(string(bedout), check.Equals, `chr1 0 248 0 500 . 0 224
-chr1 224 372 1 250 . 248 348
-chr1 348 496 2 0 . 372 472
-chr1 472 572 3 0 . 496 572
-chr2 0 248 4 750 . 0 224
-chr2 224 372 5 0 . 248 348
-chr2 348 496 6 500 . 372 472
-chr2 472 572 7 0 . 496 572
+chr1 224 372 1 1000 . 248 348
+chr1 348 496 2 1000 . 372 472
+chr1 472 572 3 1000 . 496 572
+chr2 0 248 4 1000 . 0 224
+chr2 224 372 5 750 . 248 348
+chr2 348 496 6 1000 . 372 472
+chr2 472 572 7 1000 . 496 572
 `)
 }