Version 2.0.0b2

This commit merges the updates branch and adds the following features:

- More generalized file handling to allow user to run with only VCF plus
BAM
- Snakemake pipeline to allow easy running
- Script to combine pipeline outputs across multiple samples
- Ability to install via pip

This is a squashed commit of the following:

commit 9dfa3e2
Author: Mike Dacre <[email protected]>
Date:   Thu May 17 14:37:28 2018 -0700

    Add pipeline components.

commit 99a9eb1
Author: Mike Dacre <[email protected]>
Date:   Wed May 16 17:37:14 2018 -0700

    Add get_snake command to cisVar.py

commit 1d7d116
Author: Mike Dacre <[email protected]>
Date:   Wed May 16 17:36:50 2018 -0700

    Make README current

commit 38e2db1
Author: Mike Dacre <[email protected]>
Date:   Wed May 16 17:36:23 2018 -0700

    Make installable with pip

commit 9f5f4db
Author: Mike Dacre <[email protected]>
Date:   Wed May 16 15:18:21 2018 -0700

    Add complete documentation

commit 10c145f
Author: Mike Dacre <[email protected]>
Date:   Wed May 16 10:57:01 2018 -0700

    Minor bugfix

commit adc73ec
Author: Mike Dacre <[email protected]>
Date:   Tue May 15 17:54:44 2018 -0700

    Add script to combine dataframes

commit 680d75b
Author: Mike Dacre <[email protected]>
Date:   Mon May 14 17:37:08 2018 -0700

    Add standardized Snakemake pipeline for cisVar

commit 2f43e29
Author: Mike Dacre <[email protected]>
Date:   Mon May 14 17:36:37 2018 -0700

    Moved external scripts into main script

commit 87e7b40
Author: Mike Dacre <[email protected]>
Date:   Mon May 14 10:52:25 2018 -0700

    Integrated outside functions to core code

commit bbc8d57
Author: Mike Dacre <[email protected]>
Date:   Mon Apr 30 16:02:03 2018 -0700

    Increase readability of the regression code

commit 0724e73
Author: Mike Dacre <[email protected]>
Date:   Tue Apr 24 17:59:49 2018 -0700

    Version 2.0.0

    Update to for POST and GENO sorting to be identical.

    Also simplify and integrate code to make it work on any dataset.

commit fe7062b
Author: Mike Dacre <[email protected]>
Date:   Mon Apr 23 16:42:43 2018 -0700

    Restructured argparse to make it more sane

commit 5694fe5
Author: Mike Dacre <[email protected]>
Date:   Wed Apr 11 10:10:10 2018 -0700

    More robust handling of the R script plus bugfixes

commit 86f82af
Author: Mike Dacre <[email protected]>
Date:   Wed Feb 21 18:13:36 2018 -0800

    Add documentation to genoExtract function

commit f55c5c0
Author: Mike Dacre <[email protected]>
Date:   Wed Feb 21 18:12:54 2018 -0800

    Minor speed bugfix

commit 81b4984
Author: Mike Dacre <[email protected]>
Date:   Wed Feb 21 18:09:30 2018 -0800

    Alter genoExtract function to check data integrity

    Also reduces memory usage from ~150GB down to ~10GB and increases
    speed from ~10 hours to ~10 minutes.

    Also added documentation to the function.

commit f7d578b
Author: Mike Dacre <[email protected]>
Date:   Wed Feb 21 13:13:29 2018 -0800

    Attempted low memory solution, too slow

commit 9c40c73
Merge: f2d9bc3 0669969
Author: Mike Dacre <[email protected]>
Date:   Tue Feb 20 11:04:49 2018 -0800

    Merge branch 'updates' of github.com:TheFraserLab/cisVar into updates

commit f2d9bc3
Author: Mike Dacre <[email protected]>
Date:   Tue Feb 20 11:04:37 2018 -0800

    Add qqlot plotting

commit 0669969
Merge: 2bbf0db 0ae247c
Author: Mike Dacre <[email protected]>
Date:   Mon Feb 12 13:38:05 2018 -0800

    Merge branch 'updates' of github.com:TheFraserLab/cisVar into updates

commit 2bbf0db
Author: Mike Dacre <[email protected]>
Date:   Mon Feb 12 13:38:02 2018 -0800

    Changes to multiprocessing

commit 0ae247c
Author: Mike Dacre <[email protected]>
Date:   Mon Feb 12 13:37:13 2018 -0800

    Bugfixes

commit d3158dc
Author: Mike Dacre <[email protected]>
Date:   Fri Jan 26 13:51:03 2018 -0800

    Minor bugfix

commit 31e5c8c
Author: Mike Dacre <[email protected]>
Date:   Wed Jan 17 15:26:02 2018 -0800

    Misc stability updates and plotting code

commit c080388
Author: Mike Dacre <[email protected]>
Date:   Mon Jan 15 16:58:10 2018 -0800

    Made genotype parsing bed and vcf compatible and more robust

commit dcad85a
Author: Mike Dacre <[email protected]>
Date:   Tue Dec 19 15:06:45 2017 -0800

    Generalized code and added progress messages

    Generalized the regression code to work with a wider range of data,
    particularly by removing or making more obvious most hard-coded limits
    in the R regression.

    Also added better progress tracking messages to all code.

    vcf_to_indi_and_geno has multiple changes to make it parrallelize
    better.

Author: MikeDacre

.gitignore

@@ -1,6 +1,10 @@
 # Ipython
 .ipynb_checkpoints
 
+# Vim
+Session.vim
+.ropeproject
+
 # Apple's junk
 .DS_Store