arcs

• Release version 1.2.6
• Bugfix for arks-tigmint and arcs-tigmint rules in arcs-make
• Update documentation

• Release version 1.2.5
• Update arcs-make to allow uncompressed long read files as input

• Release version 1.2.4
• Remove integrated btllib, make it a dependency

• 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

• 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

• Release version 1.2.1
• Added arcs-make to tar.gz

• 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

• 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

• 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 option 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

Big fixes
Improved documentation
Better input error handling

• Fix whitespace errors in makeTSVfile.py

• Do not trim lower-case characters from the ends of sequences.

• Use BX tag by default if present. The option --bx now has no effect.
• Read the FASTA sequence lengths from the SAM header.

• 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 on 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)

• Release version v1.0.1
• added --dist_est option to estimate gap sizes
  • distance estimations are based on number of shared Chromium barcodes between contig head/tail regions that flank the gap
• 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