Changelogs » Hicstuff



* PCR filter now works as expected (removes all fragments with both reads at exact same coordinates except 1)
* scalogram now accepts genomic coordinates for range and index options


* Fixed a bug that crashed `hicstuff view` when computing a matrix ratio without using -n and -l.
* Fixed a bug in `hicstuff pipeline` that caused some pairs not to be flipped correctly
* Added support for pairs files as input in `hicstuff distancelaw`


Resolve bug that lost chromosome order when using hicstuff view --region if their names did not follow alphanumeric order.


Add feature to filter pcr duplicates:

* Can be enabled with the `-D` / `--duplicates` flag in the command `hicstuff pipeline`.
* python function `filter_pcr_dup` in can be used directly on a pairs file.


:warning:  Intoduces non-backwards compatible changes to the CLI:
* Option `-m, --minimap2` becomes `-a, --aligner`, taking either "minimap2" or "bowtie2" as value
* Option `-f, --fasta` becomes `-g, --genome`

Changes in behaviour:
* `-g` must be a fasta file when using minimap2, and a bowtie2 index prefix when using bowtie2
*  A fasta file is created among temporary file when using bowtie2. It is generated from the bt2 index.