From a8f7234aff7e9090161e3c745d3daf46098f57e0 Mon Sep 17 00:00:00 2001 From: Philipp Benner Date: Sun, 29 Sep 2024 14:23:18 +0200 Subject: [PATCH] 2024/09/29-14:23:18 (Linux cray unknown) --- tools/bamView/bamView.go | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/tools/bamView/bamView.go b/tools/bamView/bamView.go index 9097d57..f5d0e79 100644 --- a/tools/bamView/bamView.go +++ b/tools/bamView/bamView.go @@ -77,12 +77,20 @@ func bamView(config Config, filenameIn string) { fmt.Println() for block := range reader.ReadSingleEnd() { + seqname := "*" + position := "*" + if block.RefID >= 0 { + seqname = reader.Genome.Seqnames[block.RefID] + } + if block.Position >= 0 { + position = strconv.FormatInt(int64(block.Position), 10) + } if block.Error != nil { log.Fatal(block.Error) } - fmt.Printf("%10s %15d %5d:%011s %4d", - reader.Genome.Seqnames[block.RefID], - block.Position, + fmt.Printf("%10s %15s %5d:%011s %4d", + seqname, + position, block.Flag, strconv.FormatInt(int64(block.Flag), 2), block.MapQ)