v1.1.1

Changes:

• Fixed executables in Docker image, which were linked using softlinks.

v1.1.0

Log of changes:

• Added the onco_extract script to infer LOH blocks in cancer setups
• Updated the Dockerfile with the vcfpy and psutil dependencies required by onco_extract
• Merged pull request #11 in master. The extract tool now properly handles phased genotypes
• Merged pull request #12 in master. The dockerfile now adds a chmod 755 command to make the executable compatible with a singularity environment

v1.0.3

Changes:

• Fixed docker plotting issues when running jloh plot using the docker image

v1.0.2

Log of changes:

• Fixed jloh stats issues when dealing with larger genomes.

v1.0.1

Log of changes:

• Fixed coloring issue in jloh plot
• Introduced --max-divergence parameter in jloh sim alongside a better reporting of the tool's progression
• Added header to LOH_candidates* files produced by jloh extract

v1.0.0

Log of changes:

• Introduced a test dataset at /test_data
• Updated plot script, now it can increase contrast of images
• Updated documentation, now available at http://jloh.readthedocs.io (growing)
• Introduced a check for BAM indexes at the beginning of jloh extract

v0.23.0

Log of changes:

• Introducing the cluster algorithm. Based on the output of multiple jloh extract runs, uses the TSV files to get a pairwise jaccard index, then converts it into a distance and makes a distance matrix from which it infers clusters.
• New addition to jloh plot: now it accepts the clusters produced by jloh cluster as input to determine the plotting order of samples.

v0.22.1

Log of changes:

• Minor change in the plotting script, now follows order of sample declaration rather than alphabetical order. This aids the user in creating plots that are relevant for their analysis.

v0.22.0

Log of changes:

• Radically changed the plotting engine and rationale. Now including a switch to either plot by sample or by chromosome. This applies to both the --one-ref and the --two-ref modes.

v0.21.0

Log of changes:

• Update in "jloh extract". Now can accept also one parental genome sequence as input and still try to assign blocks to REF or ALT. This mode is turned on with the new option --one-parent, and it is different from the default, in which no annotation is attempted.
• Default "jloh extract" mode now returns "-" in the Allele column of the blocks tsv file, to highlight the fact that no annotation was attempted and differentiate it from the --one-parent mode.
• Changed "jloh plot" plotting function from geom_raster() to geom_tile() to handle also very small window sizes. The previous version did not handle correctly runs with --window 100.
• "jloh plot" now handles two types of input: --one-ref and --two-ref, which corresponds to the usage (or not) of the new --one-parent mode of "jloh extract".