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Genomicus / bedtools

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Warnings should go into STDERR, not STDOUT #137

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
I noticed the problem with complementBed, but i guess it's a bedtools-wide 
issue. The "gene.protein_coding.bed" mentioned in the command line below 
contains erroneous out-of-chromosome entries.
The command is:
$ complementBed -i gene.protein_coding.bed -g ~/chromInfo_hg19.txt > 
intergenic.bed

What is the expected output? What do you see instead?
output (i.e. file named "intergenic.bed") should be pure BED format. Here's 
what i get instead:
[...]
chr7    152495462       152500739
chr7    152509964       159138663
Warninge: end of BED entry exceeds chromosome length. Please correct.
chrX    155648238       155806176

This warning should definitely go into STDERR.

What version of the product are you using? On what operating system?
2.15.0 on linux 2.6.31.5-127.fc12.x86_64

Please provide any additional information below.

Original issue reported on code.google.com by julien...@gmail.com on 30 Aug 2012 at 9:46

GoogleCodeExporter commented 9 years ago 
Thanks, this has been corrected in the github repository.

Original comment by aaronqui...@gmail.com on 30 Aug 2012 at 12:13