Release 1.5.a: Memory fixes

This release fixes memory leaks and a memory access error that would happen only on some architectures.

Changelist:

• Fixed memory access error when output file path contained keyword ".csv" (and probably on other cases too)
• Fixed memory leaking at exit of 3 blocks
• Reduced number of percentage completion prints by 5

Release 1.4: support for ids and names in fine-grained comparisons and other fixes

With this release CHROMEISTER now supports names (and numeric ids) in the fine-grained comparisons that can be generated in conjunction with the inmemory_guided_chrom branch of GECKO.

Changelist:

• Added name and id support on the fine grained master csv files (see README)
• Fixed error where grid execution would not add sequence length to the raw matrix txt, causing an error
• Improved README with further examples

Release 1.3.c: Now events have color!

This release includes the addition of colors for each event detected in the rearrangements detection. These are:

    # conserved blocks  = Red
    # inverted blocks   = Green
    # transposed blocks = Blue

Changelist

• Added colors
• Fixed classification of conserved blocks, which were being calculated with global coordinates

Release 1.3.b: added python autoexecutable in events

This release improves integration with bioconda by making the python script detect_events.py executable

Release 1.3.a: new events detection system!

This new release includes a completely new and reworked events detection system. Previously, blocks were classified using a custom recursive growing regions algorithm, now it is based on the Hough transform from the cv2 python library. It is faster and has much more sensitivity detecting blocks.

Changelist

• Added new detection system based on houghs transform
• Added documentation
• Changed run_and_plot script to include new changes
• Removed old testing data
• Included field strand in the events file

Release 1.2 important grid fix

This release fixes the previously-reported error:

Error in axis(1, tick = FALSE, labels = seq_x_labels, at = seq_x_ticks)

Release 1.1.1: improving outputs and functionality!

This release 1.1.c comes with improved functionality.

Fixes:

1. The ending score print of both grid and no-grid scripts no longer has annonying brackets around
2. Removed newline in the no-grid script that caused further scripts to crash
3. Removed "null line" print in score scripts

Release 1.1.b with further documentation

In this release we have included further documentation to account for example runs both with and without grid, including single pairwise and multi-fasta comparison.

Fixes:

1. Changed names in the test-data folder to those auto-generated

Release 1.1.a

This release fixes the setting of CC in the compilation.

Release CHROMEISTER 1.1

This release fixes the exit status code in the help section of the previous CHROMEISTER release.

Additions:

1. Included test folder with two mycoplasmas
2. Included test folder

Fixes:

1. Changed status of exit code in help command
2. Included missing library in commonFunctions
3. Improved compatibility in makefile