HICUP v0.9.2

HiCUP v0.9.2 is a minor update incorporating the change described below:

• Updated documentation

HICUP v0.9.1

HiCUP v0.9.1 is a minor update incorporating the change described below:

• hicup2homer conversion script is now executable.

• fixed bug in scribl_capture_ditag_sorter.pl caused by non-Linux line
  endings. The script now runs.

HiCUP v0.9.0

HiCUP v0.9.0 is a major update incorporating the changes described below:

• hicup2juicer script may now be passed the parameter --digest which
  enables users to retrieve the fragment ID instead of the dummy values
  0 and 1 (contributed by https://github.com/lldelisle)

• hicup2juicer script may be passed the parameter --usemid which results
  in the position in the middle of the restriction fragment being
  reported instead of the 5' end
  (contributed by https://github.com/lldelisle).

• Added scripts for processing SCRiBL datasets.

HiCUP v0.8.3

HiCUP v0.8.3 is a minor update incorporating the change described below:

• Updated contact details

HiCUP v0.8.2

HiCUP v0.8.2 is a minor update incorporating the change described below:

• The get_captured_reads script has been renamed to hicup_capture. The script is found in the Misc folder and is used to identify "captured" di-tags in a Capture Hi-C experiment. The renamed script now works in both the Misc directory or in the same directory as hicup_module (which is useful for Conda installs or when creating symbolic links to the hicup_capture script).

HiCUP v0.8.1

RELEASE NOTES FOR HICUP v0.8.1 (16 FEBRUARY 2020)

HiCUP previously could not process Gzipped files when run on a Mac computer. While HiCUP is designed for Linux systems, a simple fix was made on how Gzipped files are uncompressed and consequently HiCUP should now work on Mac systems.

HiCUP v0.8.0

RELEASE NOTES FOR HICUP v0.8.0 (08 OCTOBER 2020)

HiCUP v0.8.0 is a major update incorporating the changes described below:

• HiCUP has a new script named hicup_reporter that collates the summary
  reports from each step of the pipeline into a new report.

Note: This hicup_reporter script can be run on its own to collate summary
results files generated previously by HiCUP.

• The pipeline generates a new HTML summary report using the script
  r_scripts/hicup_reporter.rmd (this script is executed by hicup_reporter).

Note: this requires the R packages Tidyverse and Plotly to be installed

HiCUP v0.7.4

-Fixed bug when specifying a cut-site containing an N (any nucleotide).
The script hicup_truncater used to incorporate such Ns into the FASTQ
truncated read. This is now fixed and no longer occurs.

-HiCUP now uses CIGAR string information when positioning reads to
restriction fragments and during the de-duplication process.

-Added scripts for GitHub Actions unit testing.

-Added a HiCUP Singularity recipe to the Misc folder.

HiCUP v0.7.3

HiCUP v0.7.3 is a minor update incorporating the changes described below:

-Added hicup2juicer to make HiCUP output compatible with Juicer

-Modification to hicup_deduplicator output so files strictly adhere to SAM/BAM format

-Fixed bug preventing --nofill option from working

-No longer reports Bowtie2 message concerning gzbuffer changes

v0.7.2

HiCUP v0.7.2 is a minor update incorporating the changes described below:

-Fixed bug causing output files to not strictly adhere to SAM/BAM format.