v1.0.0

Completely replaced the build system. The new build system is based on the GNU Autotools. See the main README for instructions on how to run the configure script.

Caution:
Please do not use the automatically generated tarballs from Github. These do not contain the bootstrapped files required by the build system. You can recognise Github releases by their file suffix (tar.gz). The correct tarball is bzipped (shorah-1.0.0.tar.bz2).

v0.8.2: Minor version that reinserts directory amplicon_test

amplicon_test directory

Minor version that reinserts directory amplicon_test deleted in a previous commit.

v0.8.1

No major changes, except that samtools (0.1.20) is again included in the software.

Version 0.8

Changes:

• slightly better logging everywhere (no log on empty calls)
• better options help
• snv.py is now called from within dec.py and so always runs
• shorah.py now selects the highest frequency haplotypes and writes
  them to a different file
• dec.py now keeps files by default and has an improved workflow,
  resulting in less problems when rerunning. Snv directories are not
  deleted when rerun
• amplian.py now runs snv.py, discovers highest entropy region and,
  with matplotlib, also plots it