Pygtftk

Bug Fixes

* *ologram* warnings are now clearer.

* Fixed reproducibility issue when using --more_keys in *ologram*.

* Fix 78 (Relaxing constraints on GTF format)

API Changes

Code changes

* Added new tests to *overlapping*.

* Excluding regions in *ologram* is now done in C++, bringing major speedups (400x).

New Features

* Added -b/--bool argument to *overlapping*.

* Added -/--annotate-all to *overlapping*.

* Added bigwig_to_bed.

* Added --bed-incl argument to *ologram*. (fix 73)

* The --dpi has been removed from *ologram*.

* The --pval-precision has been removed from *ologram*.

* The --user-img-file argument in *ologram* has become pdf_file.

* Added -W as command-wise argument. It force gtftk to print its
message to a file. This may be handy when no access to stderr
is available (e.g. through a scheduler).

This version provides several improvements and bug fix to ologram. The CLI of *mk_matrix*
and *join_multi_file* have slightly changed. An int ([0-4]) is now mandatory to control
verbosity level.

Bug Fixes

* Fix 76 (issue with chromosomes in ensembl format when using ologram).

* Fix 72 (P-values equal to zero when nb_intersections_true and
nb_intersections_expectation_shuffled are equal to zero).

API Changes

Code changes

* Improved p-value precision in ologram.

New Features

* Added -j/--sort-features to ologram. Controls the feature sorting in
barplot diagram. Changed doc accordingly.

* The positional argument 'bigwiglist' in mk_matrix has been replaced by -y.

* The verbosity argument now must take a value (0-4).

* The positional argument in join_multi_file has been replaced by -m.

* Updated changelog

Bug Fixes

API Changes

Code changes

New Features

* Improved p-value precision in ologram.

Bug Fixes

API Changes

Code changes

* Improved p-value precision in ologram.

* Added mpmath as dependency.

New Features

* Added tiny_real dataset.

* Added -q argument (--quiet) to get_example.

* No more using readthedoc as the doc is becoming too long to process.

Bug Fixes

API Changes

Code changes

* Many typo detected and fixed.

New Features

* Added tiny_real dataset.

* Added -q argument (--quiet) to get_example.

Bug Fixes

* Fix --no-strandness in divergent.

API Changes

Code changes

* Many typo detected and fixed.

New Features

* This version now integrates ologram (OverLap Of Genomic Regions Analysis using
Monte Carlo). Ologram annotates peaks(in BED format) with region sets/features
extracted from (i) GTF file features (e.g promoter, tts, gene body, UTR...) (ii)
GTF file keys (e.g. gene_biotype, user defined keys...) (iii) or from a BED file.

* The user can now use --chrom-info to provide the command with a file or a string.
The string should be one of 'mm8', 'mm9', 'mm10', 'hg19', 'hg38', 'rn3' or 'rn4'.
When a genome version is requested as a string, the conventional chromosomes
are used (chrM is discarded together with alternative haplotypes,
unlocalized regions...).