Tom Conway

quoting strings composed of digits

31

Hi, Consider the following program: ```python import sys import yaml w = {'userName': 'scientist ', 'userEmail': '[email protected]', 'sampleName': '08063075', 'fastqDir': '/foo/bar/baz/171108_M00139_0253_000000000-BHFD5/ProjectFolders/Project_Qux-Wombat-/Sample_08063075', 'analysis': 'Somatic_Run375_MY_DY_08112017', 'laneNo': 1, 'panel': 'Somatic_Panel_Manifest_v4_23_10_2015'} yaml.dump(w, sys.stdout, default_flow_style=False)...

Hi Bpipies, At the moment, when using containered execution (e.g. `singularity`), it is possible to bind extra paths to make them visible inside the container, using a filesystems declaration block....

Great library, thanks for making it! I am writing succinct data structure code using `pdep` to implement `select` on 64-bit words: ```rust pub fn select64(x: u64, idx: usize) -> u64...

Tolerant VCF parsing

3

G'day. Thanks for making a nice tool. I'm trying to use `vcfanno` (0.3.5, linux binary) with a large combined VCF of gnomad v3.1. The combined bgzipped file is ~2TB, so...

I'm wanting to use boost::iostreams::restrict to present parts of a file given as an istream as if they were first class istreams. My first test case which works on an...

choose pileup call over full-alignment call if pileup call has 1) a way higher QUAL, 2) is an indel

6

Hi! Thanks for making a good tool! We have been doing testing and benchmarking with (clinical) trio data, and have found a corner case where the behaviour of the merge...

VCF header error

5

Thanks again for developing a terrific library! I am parsing a VCF what contains the following header lines (with the bulk of each removed for clarity: ``` ... ##GATKCommandLine= ##GATKCommandLine=...

Question about SyncmerIterator

4

Hi, I'm studying your implementation of `SyncmerIterator`, and I'm a bit confused. It's possible there's a bug in the code, but I think it's much more likely that I just...

Hi GATK, We appear to have run in to a very rare corner case in `CombineGVCFs` that causes it to produce incorrect output. Unfortunately our input data is clinical, so...

Trivial fix: serialise `None` as `.`, rather than `None`.