Release Notes

Version 0.8.7 (01/19/2023)

  • Made the program compatible with pairtools v1.0.2

Version 0.8.6 (05/24/2022)

  • Added support for other 3C-based experiments that do no use restriction enzymes for DNA fragmentation

Version 0.8.5 (08/15/2021)

  • changed the default read aligner to chromap

  • made the fragment-level filtering optional

  • removed the “-O/–outformat” argument

Version 0.8.4-r1 (01/16/2021)

  • Added the “–high-res” option to runHiC pileup and runHiC binning.

Version 0.8.4 (01/03/2021)

  • Changed the bwa parameters from “bwa mem -SP” to “bwa mem -SP5M”

  • Changed the default walks policy from “mask” to “all”

  • Fixed a bug pertaining to the FASTQ read format. In previous versions, error will occur when there is “.” in the prefix of FASTQ file names.

  • Added a piechart function to runHiC quality.

  • Added a function to automatically output mcool in the final step.

  • Added a function to automatically check and remove invalid link files within the “filtered” sub-folder

  • Fixed a bug to avoid duplicate operations when only one replicate exists

  • Added a function to automatically sort chromosome names. Numerical labels will be sorted natually; for non-numerical labels, give priority to XYM over the rest.

Version 0.8.3 (03/04/2019)

  • Parallelized statistics collecting

  • Reduced the computational overhead in the filtering step

Version 0.8.2 (01/16/2019)

  • Fixed a bug pertaining to large dataset overflow in binning (by increasing the value for --max-split)

Version 0.8.1 (12/23/2018)

  • Added support for Arima Hi-C

Version 0.8.0 (09/16/2018)

  • Migrated to Python 3 (will not support Python 2 anymore)

  • Changed the data container from HDF5 to Pairs and Cooler

  • Added two aligner options: bwa-mem (short reads) / minimap2 (long reads)

  • Added options to output filtered SAM/BAM for further analysis

Version 0.7.0 (10/29/2017)

  • Parallelized the execution on both laptops and PBS-based clusters.

  • Included the latest mirnylib and hiclib source code.

  • Tuned the class/function interfaces in sync with the lastest hiclib.

  • Removed the visualize subcommand.

  • Changed the default “–chroms” setting to “[‘#’,’X’]”

  • Refined the logging information.

  • Added the detailed documentations.

Version 0.6.6-r2 (05/04/2016)

  • Fixed a bug related to “–bowtieIndex”.

  • Included LICENSE.

Version 0.6.6-r1 (11/10/2015)

  • Only check for update when you are online.

Version 0.6.6 (11/06/2015)

  • Removed redundant command-line arguments.

  • Added detailed descriptions for the quality assessment module in Recipes.rst.

  • Added snippets for automatic update checking.

Version 0.6.5 (09/29/2015)

  • More sophisticated quality assessment module.

  • Changed the filtering settings for pileup.

  • Redirected the exception information into the log file.

Version 0.6.4 (09/21/2015)

  • Fixed a bug related to the metadata loading.

Version 0.6.3 (09/16/2015)

  • Customized the mirnylib Genome class by overriding the _extractChrmLabel method.

Version 0.6.2 (08/21/2015)

  • Added the visualize subcommand.

Version 0.6.1 (07/21/2015)

  • Improved the logging system.

Version 0.6.0 (06/16/2015)

  • Fixed a bug for bam file parsing in the case of FASTQ read format.