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NEWS
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Package: CostelloJPSCNSeq
=========================
Version: 0.6.0-9000 [2021-02-20]
SIGNIFICANT CHANGES:
* Renamed argument 'binSize' for pscnseq_pscbs() to 'binsize'.
NEW FEATURES:
* Made it easier to call pscnseq() from the command line, e.g.
'Rscript -e CostelloJPSCNSeq::pscnseq --args --help' and
'Rscript -e CostelloJPSCNSeq::pscnseq --args --config=/path/to/config.yml'.
BUG FIXES:
* pscnseq() did not output session details in batch but in interactive mode.
Version: 0.6.0 [2021-02-10]
SIGNIFICANT CHANGES:
* Add master function pscnseq().
* Turned pipeline scripts into an R package.
* Pipeline updated to use R 3.6.1.
DOCUMENTATION:
* Added help pages for pscnseq(), pscnseq_mpileup(), pscnseq_pscbs(),
pscnseq_sequenza(), and pscnseq_reports().
BUG FIXES:
* Argument 'value' for future::resolve() was deprecated in favor of 'result'.
DEPRECATION & DEFUNCT:
* Dropped support for BatchJobs; use batchtools instead.
Version: 0.5.1 [2019-07-28]
DOCUMENTATION:
* There was a typo in Section 'Configure parallel processing' of the
README.md causing the batchtools.torque.tmpl file to end up in the
wrong location if one cut'n'pasted the call.
SOFTWARE QUALITY:
* Use `/usr/bin/env bash` shebangs in PBS scripts rather than `/bin/bash`.
Version: 0.5.0 [2019-04-23]
SIGNIFICANT CHANGES:
* Pipeline updated to use R 3.5.2.
NEW FEATURES:
* 1.mpileup.R now asserts that BAM files have been indexed, that
is, there exist corresponding BAI files.
SOFTWARE QUALITY:
* PBS scripts are now validated using ShellCheck. Fixed a few
potential issues but nothing that looked like bugs.
* R script are now validated to be parsable.
Version: 0.4.2 [2018-12-05]
Version: 0.4.1 [2018-05-28]
Version: 0.4.0 [2018-05-24]
Version: 0.3.1 [2018-05-12]
Version: 0.3.0 [2017-06-26]
Version: 0.2.3 [2017-06-19]
Version: 0.2.2 [2017-02-28]
Version: 0.2.1 [2016-11-02]
Version: 0.2.0 [2016-11-02]