Notes for Arioc v1.50:

The current build is v1.50.3065 (10 February 2022).

This is a stable, performance-tested build.

Arioc v1.50 reference-genome lookup tables are incompatible with those generated by AriocE in release v1.43 and earlier. If you are upgrading to v1.50 from an earlier version of Arioc, please re-execute AriocE to create new lookup tables. Updated lookup tables for the human, mouse, and bread yeast reference genomes are available at ftp:https://ftp.ccb.jhu.edu/pub/data/Arioc, the FTP server for the Center for Computational Biology at Johns Hopkins University.

New features

• AriocE: support FASTA-formatted reference files that contain multiple individually-identified subunits (chromosomes, genomes, DNA regions)
• AriocE: support for SAM fields defined in FASTQ definition lines and subsequently appended to SAM alignment records
• XMC: added MAPQ, TLEN, and AS distributions

Bug fixes

• AriocU, AriocP: incorrect behavior with suppressRaggSQ
• AriocE: buffer overflow with very short reference genomes
• Linux and Windows examples: spurious maxA parameter in AriocU and AriocP configuration files for GRCh38
• AriocU, AriocP: incorrect SEQ sporadically reported for reverse-complement reads whose length is an exact multiple of 21

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