julianhess

Use system htslib; a couple minor tweaks

2

The htslib submodule was getting stale; I think it's better if we use whatever system htslib is already included. Also implemented a more efficient way of getting the number of...

samtools cat fails if the first argument is a stream

1

#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib] Yes, v1.16.1 #### Please describe your environment. Ubuntu 20.04.2 LTS ``` $ uname -sr Linux 4.4.0-210-generic $ uname -m...

More robustly handle sample names in indel VCF headers

1

The VCF spec demands that the samples' column names match entries in the header (e.g. if `##normal_sample=MY_NORMAL` is present in the header, then the column for the normal should be...

Update submodules to work with GCC 10

4

Fixes https://github.com/walaj/SeqLib/issues/66

Hi Jeremiah, New versions of GCC choke on the current bwa/fermi-lite submodules, due to an issue fixed in the following commit: https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284 (there is not a complementary commit in fermi-lite,...

Hi, Great work, but having all your code in ZIP files makes it very hard to browse on GitHub. I unzipped everything so people can actually view your code without...