Martin Mokrejš

nanopolish --version from git checkout shows wrong version number (of a last release?)

1

Hi Jared, if I build nanopolish from git HEAD the binary gives me now: $ /usr/bin/nanopolish --version nanopolish version 0.7.1 Written by Jared Simpson. Copyright 2015-2017 Ontario Institute for Cancer...

Please provide LICENSE and Makefile files and update README.md

1

Dear Heng, I wanted to make a package for Gentoo Linux but I lack the above two files. Use ``` CXX ?= g++ CXXFLAGS ?= -O2 CPPFLAGS ?= -Iinclude ```...

oea should warn if minThreads is set > 1

2

Hi, I had to restart `canu` jobs a few times. Provided canu remembers the initial configuration at each step because the partitioning happens only once in each pipeline step and...

2.1.1: overlapInCorePartition generates 67GB large shellscript full of just if and fi

12

Hi, it happened to me that `overlapInCorePartition` generated too many partitions and a 67GB large `correction/1-overlapper/overlap.sh` shellscript, practically just huge if/else code which a call to perl utility afterwards. Interpreting...

Using $TMPDIR for fast local sorting using ovStoreSorter

5

Hi, would it be possible to implement what you proposed in https://github.com/marbl/canu/issues/705#issuecomment-344597980 in point nr. 2? My problem is is that on a 2TB RAM machine `canu-2.1.1/build/bin/ovStoreSorter` was run per...

Error: Type checker found wrong number of fields while tokenizing data line.

6

Hi, would it be possible to improve `bedtools` (have v2.29.2 now) to output a line number of line contents where thsi check fails? I just cannot find. Tabs are in...

Hi, I cannot find who calls the script `src/utils/BamTools/mapping/BamAlignment.py` but seems the print call needs adjustment for python3 syntax. (As of bedtools-2.29.2).

effstring.t03 test fails

1

Hi, I just installed gemini and ran the test suite but it fails with: ``` effstring.t03...\c 0a1 > CCNL2 5_prime_UTR_variant LOW protein_coding 1 0 0 12d12 < CCNL2 5_prime_UTR_variant LOW...

Hi, I just installed gemini and ran the test suite but it fails with: ``` cadd.t01...\c 2,4c2,4 < chr1 30859 30860 G C -0.05 1.96 < chr1 69269 69270 A...

Hi, I just installed gemini and ran the test suite but it fails with: ``` nogls-sub-bcolz.t14...\c 5d4 < chr1 1220953 1220954 G A SCNN1D G/G G/G fail ``` The last...