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2024-11-05 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.8
* Add optional parameter 'prefix' to `arcs-make` - if specified, soft-links the final scaffolds fasta file to a file with this prefix
* Update documentation
2024-03-25 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.7
* Update `arcs` version message
* Update e-mails, copyright years
2023-12-06 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.6
* Bugfix for `arks-tigmint` and `arcs-tigmint` rules in `arcs-make`
* Update documentation
2023-01-05 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.5
* Update `arcs-make` to allow uncompressed long read files as input
2022-06-03 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.4
* Remove integrated btllib, make it a dependency
2022-02-11 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.3
* Add arcs-make, makeTSVfile.py to 'bin' folder
* Add `-I` option to minimap2 for arcs-long target to avoid
splitting index if genome size large
* Set to 50G by default, can be changed using `minimap2_index_size`
* Update documentation
* Bugfixes
2021-05-28 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.2.2
* long-to-linked-pe script ported to C++
* pseudo-linked reads are streamed directly from long-to-linked-pe to
`arcs --arks` in ARKS-long mode
* Bugfixes
2021-01-29 Theodora Lo <tlo@bcgsc.ca>
* Release version 1.2.1
* Added `arcs-make` to `tar.gz`
2021-01-19 Theodora Lo <tlo@bcgsc.ca>
* Release version 1.2.0
* Users can now also use long reads to scaffold draft assemblies
* Added `--arcs-long` and `--arks-long` modes to `arcs-make` so
users can run the ARCS+LINKS pipeline using long reads as input
* `long-to-linked-pe` segments and assigns barcodes to the long
reads prior to running ARCS and LINKS
2020-01-08 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.1.1
* Users can now set the --pair parameter to output a tsv file with the
number of links supporting each orientation (hh, ht, th, tt) of each
scaffold pair
* Bug fix to binomial test
2019-09-09 Lauren Coombe <lcoombe@bcgsc.ca>
* Release version 1.1.0
* Integrates 'ARKS' code (https://github.com/bcgsc/arks) into ARCS
* Now, can run ARCS in either default mode (using linked read
alignments) or ARKS mode (using exact k-mer mapping)
* added `--arks` mode to run in ARKS mode
* Updated `arcs-make` to specify in which mode to run the
scaffolding with linked reads
* Bug fix to calculation of barcode multiplicity
2019-05-13 Rene Warren <rwarren@bcgsc.ca>
* Big fixes
* Improved documentation
* Better input error handling
2018-07-31 Ben Vandervalk <benv@bcgsc.ca>
* Release version 1.0.5.
* Fix whitespace errors in makeTSVfile.py
2018-06-20 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.0.4.
* Do not trim lower-case characters from the ends of sequences.
2018-04-13 Shaun Jackman <sjackman@bcgsc.ca>
* Release version 1.0.3.
* Use BX tag by default if present. The option `--bx` now has no effect.
* Read the FASTA sequence lengths from the SAM header.
2018-03-12 Ben Vandervalk <benv@bcgsc.ca>
* Release version v1.0.2
* added `--bx` option to parse Chromium barcodes from BX tag
* fixed `makeTSVfile.py` for improved handling of distance
estimates in LINKS v1.8.6 or later. The ARCS `--dist_est`
option must be turned for distance estimates to be generated
and used downstream by LINKS.
* fixed incorrect default value of `--end_length` (0 => 30000)
* fixed `--graph` option to output vertex declarations in
same order as input FASTA (ABySS compatibility fix)
2017-12-04 Ben Vandervalk <benv@bcgsc.ca>
* Release version v1.0.1
* added `--dist_est` option to estimate gap sizes
* distance estimations are based on number of shared Chromium
barcodes between neighbouring contig head/tail regions
* added unit tests (`make check`)
* added `--tsv` option to output graph in TSV format
* added `--barcode-counts` option to output number of
reads per barcode in TSV format
2016-09-15 Sarah Yeo <syeo@bcgsc.ca>
* Release version v1.0.0