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FastaFromBed error when a chr is not in the genome #123

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1.BED files with chrs not in the genome
2.
3.

What is the expected output? What do you see instead?
stop working

What version of the product are you using? On what operating system?
lastest

Please provide any additional information below.

It would be good to ignore these cases not exit.

Original issue reported on code.google.com by lorena.p...@gmail.com on 5 Jun 2012 at 11:51

GoogleCodeExporter commented 9 years ago 
What version are you using?  Version 2.16.2 has the behavior you want:

$ cat test.fa
>chr1
aaccttacaga

$ cat test.bed
chr1    3   6
chr2    3   6

$ bedtools getfasta -fi test.fa -bed test.bed -fo stdout
>chr1:3-6
ctt
WARNING. chromosome (chr2) was not found in the FASTA file. Skipping.

Original comment by aaronqui...@gmail.com on 6 Jun 2012 at 3:53

GoogleCodeExporter commented 9 years ago 
oh! sorry ,  2.14. I was told I have the last. 

thanks a lot. The next time I will post in the group, not here.

thanks

Original comment by lorena.p...@gmail.com on 6 Jun 2012 at 4:07

GoogleCodeExporter commented 9 years ago

Original comment by aaronqui...@gmail.com on 6 Jun 2012 at 4:35