From 64b1a37b5ed62a1b32ea168c99d8899c049f2b9a Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Thu, 30 Jan 2020 10:01:57 -0500 Subject: [PATCH] Fix writing all variant numbers to npy row 0. Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- gvcf2numpy.go | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/gvcf2numpy.go b/gvcf2numpy.go index 2ef1dfd65a..5a02584618 100644 --- a/gvcf2numpy.go +++ b/gvcf2numpy.go @@ -237,12 +237,14 @@ func (cmd *gvcf2numpy) printVariants(tseqs []tileSeq) error { } } } - out := make([]uint16, len(tseqs)*int(maxtag+1)) - for i := 0; i < len(tseqs)/2; i++ { + rows := len(tseqs) / 2 + cols := 2 * (int(maxtag) + 1) + out := make([]uint16, rows*cols) + for row := 0; row < len(tseqs)/2; row++ { for phase := 0; phase < 2; phase++ { - for _, path := range tseqs[i*2+phase] { + for _, path := range tseqs[row*2+phase] { for _, tvar := range path { - out[2*int(tvar.tag)+phase] = uint16(tvar.variant) + out[row*cols+2*int(tvar.tag)+phase] = uint16(tvar.variant) } } } @@ -252,7 +254,7 @@ func (cmd *gvcf2numpy) printVariants(tseqs []tileSeq) error { if err != nil { return err } - npw.Shape = []int{len(tseqs) / 2, 2 * (int(maxtag) + 1)} + npw.Shape = []int{rows, cols} npw.WriteUint16(out) return w.Flush() } -- 2.39.5