pysam-0.15.4 does not cgat-apps tests

[sebastian-luna-valero]

Please check output here: https://travis-ci.org/cgat-developers/cgat-apps/builds/646576648

That's why pysam has been pinned on this repo to version 0.15.2.

Until the tests pass, I propose to pin pysam<=0.15.2 in the cgat-flow repository as well: https://github.com/cgat-developers/cgat-flow/pull/128

[Acribbs]

Have tested 0.15.4 and the linux build works but not the Mac, seems like there is a problem with libhts https://travis-ci.org/github/cgat-developers/cgat-apps/jobs/687998165. There is a similar issue here https://github.com/bioconda/bioconda-recipes/issues/15415 but still haven't come up with a solution yet.

[Acribbs]

Hmm testing the pr worked so I merged changes. However, the testing of the master branch is giving errors again for Mac build. Given that it is only the Mac build affected and seems intermittent I won't revert the merge. I will look into this further.

Attempting to rebuild cgat-apps Conda package here: https://github.com/bioconda/bioconda-recipes/pull/22207

[Acribbs]

Actually I think I will end up reverting the merge. Its consistently breaking Mac build and I can't get Conda to package

[Acribbs]

Now testing is working this can be closed, but I will look further into why pysam output is different with later version of pysam