Steffen Möller

Without that dependency, many build errors pop up: ``` /home/moeller/git/med-team/vdjtools/vdjtools/src/main/java/com/antigenomics/vdjtools/misc/MathUtil.java:32: error: package org.apache.commons.math3.special does not exist import org.apache.commons.math3.special.Gamma; ^ /home/moeller/git/med-team/vdjtools/vdjtools/src/main/java/com/antigenomics/vdjtools/misc/MathUtil.java:33: error: package org.apache.commons.math3.util does not exist import org.apache.commons.math3.util.FastMath; ^ /home/moeller/git/med-team/vdjtools/vdjtools/src/main/java/com/antigenomics/vdjtools/misc/StatUtil.java:3:...

Hello, I am doing my best to get the pigx-rnaseq workflow to install locally. Sadly, pigx' test routines bail out with a complaint on a missing sa.bin file as part...

Hello, Please kindly have a look. I presume that the time fixing this pay off easily when there are error reports. :o) Steffen ``` g++ -o src/nanopolish_call_variants.o -c -g -O2...

Upload of ghdl-yosys-plugin to Debian?

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Hello, both ghdl and yosys are in Debian, but to the best of my understanding this connective plugin is not. Would this be supported from your side? While I could...

build test fails for intersect

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Hello, all fine, very silent, except for ``` Testing bedtools intersect: intersect.t01...ok ... intersect.t82...ok intersect.new.t01...ok ... intersect.new.t08...ok intersect.new.t09...[E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 1 ok intersect.new.t10...[E::sam_parse1] missing...

Python deprecation warnings with 3.8

1

Hello, shout out if you prefer patches. The dendropy one is not your immediate business - anyway. Regards, Steffen ``` gubbins/python/gubbins/common.py:537: DeprecationWarning: invalid escape sequence \d elif re.match('^\d', vcf_line) is...

Please tag release to allow compilation of minia

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Hello, I found https://github.com/GATB/gatb-core/commit/7cb8a48cc958f4266c74db57f02e937d583ba9b7 suggesting that this is synced with minia development, and indeed compiling minia with the latest release gives ``` /home/moeller/git/med-team/minia/minia/src/Minia.cpp:170:65: required from here /home/moeller/git/med-team/minia/minia/src/Minia.cpp:312:62: error: ‘class gatb::core::debruijn::impl::GraphUnitigsTemplate’...

Request for copyright information for all *.{h,cpp} files

1

Dear Bill, as time permits, please kindly add a copyright statement where there is none, yet. I happily perform that presumed routine work over here and send a pull request...

Hello, the clean just failed since the find_orb directory did not yet exist in my home directory. It is somewhat unexpected to see a clean target act outside the source...