ARCS v1.2.7

• Release version 1.2.7
• Update arcs version message
• Update e-mails, copyright years

ARCS v1.2.6

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

ARCS v1.2.5

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

ARCS v1.2.4

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

ARCS v1.2.3

• 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

ARCS v1.2.2

• 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

ARCS v1.2.1

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

ARCS v1.2.0

• 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

ARCS v1.1.1

• 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

ARCS v1.1.0

• 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