BBMap 38.69: trouble parsing BGZIP version
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#23 BBMap 38.69: trouble parsing BGZIP version
Hi,
Using BBMap v. 38.69 on Ubuntu Linux I'm receiving
Warning - trouble parsing BGZIP version: 1.7-2
I belive the error occurs on line #1526 in file bbmap/current/dna/Data.java where you are attempting to split the version string on the presence of a period (".").
My current version of bgzip (1.7-2, Ubuntu 18.04) uses a dash ("-") in the version string.
Split could possibly be done on "period or a dash".
Cheers
Johan N
When I encountered this problem running my jobs on a LINUX HPCC, with jobs submissions managed by SLURM manager, I simply loaded samtools module first, followed by BBMap, and this warning / error immediately went away. Good luck!
The version number string in bgzip derives from the version.sh script in htslib, and is set when running make. Their (htslib) numbering scheme is X.X.X. It's the Ubuntu people who changes the version to include a dash (in the bgzip provided in Ubuntu package libhts2). However, since there might be a few users who uses the package provided by Ubuntu, taking an extra step in BBmap (check "period or dash") might be worth the effort?
I have fixed this in the current release (38.70), using jnylander's suggestion. Thanks!