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Many scripts use "dumb" relative paths.

Status: Open.

#50 In koadman/proxigenomics;

· cerebis opened on Dec 1, 2015

external binaries using path relative to invocation directory

Status: Open.

#49 In koadman/proxigenomics;

· cerebis opened on Dec 1, 2015

Simulation pipeline requires an overarching point of entry

Status: Open.

#47 In koadman/proxigenomics;

· cerebis opened on Nov 13, 2015

External dependencies and overall structure a mess.

Status: Open.

#45 In koadman/proxigenomics;

· cerebis opened on Nov 9, 2015

Permutation control split over both file existence and parameter settings

Status: Open.

#44 In koadman/proxigenomics;

· cerebis opened on Nov 9, 2015

bam2edges and edges2metis should be combined.

Status: Open.

#43 In koadman/proxigenomics;

· cerebis opened on Oct 28, 2015

Ideally, our generated internal files should have annotation fields.

Status: Open.

#40 In koadman/proxigenomics;

· cerebis opened on Oct 27, 2015

bcubed.py does not notice when supplied the wrong file format.

Status: Open.

#39 In koadman/proxigenomics;

· cerebis opened on Oct 27, 2015

add support for running pipeline outside $HOME

Status: Open.

#38 In koadman/proxigenomics;

· koadman opened on Oct 16, 2015

binaries required by mktree.sh are unavailable

Status: Open.

#37 In koadman/proxigenomics;

· koadman opened on Oct 16, 2015

Support both Hi-C and meta3C read simulation

Status: Open.

#36 In koadman/proxigenomics;

· cerebis opened on Sep 8, 2015

Large files and method of parsing BAM

Status: Open.

#35 In koadman/proxigenomics;

· cerebis opened on Jul 30, 2015