New output format for bedtools getfasta -name

[sven.sc...@novartis.com]

Hi,

It seems that the output format for bedtools getfasta -name was changed:

chbscl-8-7: [~] $ cat test.fa
>chr1
AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG
chbscl-8-7: [~] $ cat test.bed
chr1    5       10      myseq
chbscl-8-7: [~] $ tools/CentOS7/bedtools/bedtools-2.29.2/bin/bedtools  getfasta -fi test.fa -bed test.bed -name
>myseq::chr1:5-10
AAACC
chbscl-8-7: [~] $

 This is very unfortunate for pipelines in which bedtools getfasta -name is used. Why was the format changed?

Best regards,

Sven

[Aaron Quinlan]

Hi Sven,

Sorry for the trouble. This change was actually to correct an earlier change that itself modified the behavior from the original. I suspect the -nameOnly option is what will produce your desired behavior.

Best,

Aaron

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[Sven Schuierer]

Hi Aaron,

Thanks a lot for letting me know. Actually, yesterday I accidentally created the help output of getfasta and realized that there is the option -nameOnly.

I would still argue that it would have been the better choice to keep the output of the -name option unchanged and add a new option, say -nameExtended (you had -name+, right?) for the new output format. In this way existing pipelines would not break.

Best regards,

Sven