Martin Mokrejš

Hi, I am looking for a proper way to get the sources of Kraken. I see there is https://ccb.jhu.edu/software/kraken/dl/kraken-1.0.tgz and there is https://github.com/DerrickWood/kraken/archive/v1.0.tar.gz . But, the contents are different. Please...

[Feat] Switch from OpenDWG toolkit to libredwg to allow work with DWG in practice

2

In https://bugs.gentoo.org/show_bug.cgi?id=893134 Mario figured out why Gentoo Linux cannot enable DWG support due to missing OpenDWG package. Please try to switch to libredwg. It takes quite some effort to figure...

Malformed XML format in CHEBI:16551

1

Hi, it seems ChEBI writes broken XML files with sharp brackets unescaped (actually should be `<` and `>` , respectively), breaking the XML syntax: ``` Debug: File CHEBI:16551.xml Traceback (most...

gcc-6.3.0: fatal error: stdlib.h: No such file or directory

1

Hi David, I am trying to stitch together a fast5 package for Gentoo Linux but it fails to compile with 6.3.0 here: ``` >>> Emerging (2 of 3) sci-libs/fast5-9999::science >>>...

Merging with gff3-capable fork of 2.2.0 version?

1

Hi Nathan, 1. are you aware of this forked repo? https://github.com/hotdogee/exonerate-gff3 which is an improved version of exonerate-2.2.0 with GFF3 format output support Maybe you could unite the efforts. 2....

``` >>> Test phase: sci-biology/btl_bloomfilter-1.2.1 Making check in Tests/AdHoc make[1]: Entering directory '/var/tmp/portage/portage/sci-biology/btl_bloomfilter-1.2.1/work/btl_bloomfilter-1.2.1/Tests/AdHoc' make BloomFilterTests ParallelFilter make[2]: Entering directory '/var/tmp/portage/portage/sci-biology/btl_bloomfilter-1.2.1/work/btl_bloomfilter-1.2.1/Tests/AdHoc' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../.. -Wall -Wextra -Werror -fopenmp -std=c++11...

Hi German, please improve the error message and print out the wrong readname. ``` bamsort SO=coordinate inputthreads=10 outputthreads=10 level=9 index=1 O=foo.refsorted.bam I=foo.bam [V] Reading alignments from source. Invalid alignment: Query...

bamsort crash at libmaus2::lz::BgzfDeflateParallel::flush

4

Hi, current git master checkout crashes for me (well even previous versions). ``` repository: https://github.com/gt1/libmaus2.git at the commit: 694c2180076cd5986fea0532b057065f905d49b5 repository: https://github.com/gt1/biobambam2.git at the commit: 5798e74558e001e33855cb93cc8bf149344b931d ``` ``` LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE==1m export LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE...

Do not crash if no argument was provided

1

Hi, I find it unusual that bamsort, bammerge and probably many other utils crash if they are executed without an argument. Please assume '-h' was passed to the utility and...

Hi, time to time bamsort gets stuck while reading input data. At other times a `top` program output is logged as the last one in logfile and bamsort keeps running...