John Marshall

Thanks. You are quite right that it would be good to document this in the `bedtools getfasta` usage display in particular — I would have been much more likely to...

This is a repeat of https://github.com/arq5x/bedtools2/issues/762#issuecomment-528844731; unfortunately it seems that the `SaveAlignment` patch in https://github.com/arq5x/bedtools2/issues/762#issuecomment-528900976 never got applied.

I'm inclined to agree re desirability of SAM master copies in ASCII. However you can get git diff and blame working for BAM files via git's `textconv` settings and e.g....

So far I've only been reacting to issues that go past in my @ga4gh news feed… but it has occurred to me that I'm risking accidentally volunteering to review _reads.py_...

> Turned out to be really simple, just had to […] make sure that pysam opens them with the `c` flag. When opening for reading with plain `"r"`, the underlying...

Yes, that's because it considers this malformed `#CHROM` header line terrifying enough that it prints the error message and aborts. Did you ever file an htslib issue about this? Then...

This is good as far as it goes, and IMHO would usefully be merged as such. Currently in bioconda there are 315 Perl packages using ExtUtils::MakeMaker and 119 using Module::Build....

With respect, the information that has been added about Module::Build is entirely not what this document's audience needs to know. The reader is packaging an existing Perl module that has...

When linking against the `-lbam` in an htslib-based samtools 1.x, you need to also link against `-lhts`. If it supported using samtools 1.x, Cufflinks's build system would do this itself;...

This will need to wait for a **bioconda-utils** update that pins htslib at 1.16.