Debug version: SAM output of CRAM file is populated with debug on pipe #328
Description
The SAM output of a CRAM file is unintentionally populated with debug lines.
- version of sambamba
sambamba 0.6.7
This version was built with:
LDC 1.1.1
using DMD v2.071.2
using LLVM 3.8.1
bootstrapped with LDC - the LLVM D compiler (0.17.4)
- version of samtools that did bam2cram
samtools 1.6
Using htslib 1.6
Copyright (C) 2017 Genome Research Ltd.
System version:
uname --kernel-release && cat /etc/system-release2.6.32-696.3.1.el6.x86_64
CentOS release 6.9 (Final)
- the command line or bash script used (feel free to shorten paths and filenames)
htsfile sampleX.aln.cramsampleX.aln.cram: CRAM version 3.0 compressed sequence data
sambamba view -C -h sampleX.aln.cram 2>/dev/null | less -SWould return SAM format on stdout:
- the header
- debug lines
cram_read_container
COPIED #2
COPIED #2
COPIED #2
cram_read_container
COPIED #3
COPIED #3
COPIED #3
...
cram_read_container
COPIED #4
COPIED #4
COPIED #4
COPIED #4
COPIED #4
COPIED #5
COPIED #69
COPIED #69
COPIED #69
cram_read_container
COPIED #5
COPIED #5
COPIED #5
COPIED #5
COPIED #5
- alignments
Looking at stderr:
sambamba view -C -h sampleX.aln.cram 2>&1 1>/dev/null | lessThe output is:
Init cram_fd* #1
Init cram_fd* #2
Init _Anonymous_25* #1
cram_read_slice (1/1)
Init cram_slice* #1
Init _Anonymous_25* #2
cram_read_slice (1/1)
Init cram_slice* #2
Init _Anonymous_25* #3
cram_read_slice (1/1)
...
Init cram_slice* #69
Init _Anonymous_5* #4
Free _Anonymous_5* #3
Free cram_slice* #3
Free _Anonymous_25* #3
The debug line on stdout is written on this line: cram/wrappers.d#L162
Problem occurs in both Zsh and Bash.