Notes for Arioc v1.24:

The current build is v1.24.2351.18110.

New features

• read-length distribution statistics in the AriocE (read encoding) component
• better memory management (larger batch sizes, more detailed error reporting) in the nongapped aligner component of AriocU and AriocP

Bug fixes

• AriocP: emit invalid FLAG bits for paired-end reads with one mate having exactly one mapping and the opposite mate having two or more mappings
• AriocU, AriocP: emit invalid XM (methylation context) map when a read's reverse complement maps to the reverse complement of the start of the reference sequence
• AriocP: emit incorrect MAPQ for paired-end mappings with dovetail orientation

Downloads

AriocSetup.msi: Windows binaries and examples
Arioc.w.124.zip: Windows source code
Arioc.x.124.zip: Linux source code
Arioc.RQA.124.zip: Linux examples

Arioc v1.23 adds support for 32-bit seed-and-extend lookup table hashing.

AriocSetup.msi: Windows binaries and examples
Arioc.w.123.zip: Windows source code only
Arioc.x.123.zip: Linux source code
Arioc.RQA.123.zip: Linux examples

Arioc v1.22 adds support for 64-bit PowerPC architecture.

(Thanks to Dr. Ruzhu Chen [IBM] and Dr. Edward S. Chen [Baylor College of Medicine] for letting us test Arioc on a Power8 system with four Nvidia P100 GPUs.)

Arioc v1.21 installation archives and source code

Arioc.RQA.121.zip: Linux examples
Arioc.w.121.zip: Windows source code only
Arioc.x.121.zip: Linux source code
AriocSetup.msi: Windows binaries and examples

Arioc v1.21 includes support for BS-seq alignments. This release also adds sample configurations for alignments with the human reference genome.

Arioc v1.20 installation archives and source code:

AriocSetup.msi: Windows binaries and examples
Arioc.w.120.zip: Windows source code only
Arioc.x.120.zip: Linux source code
Arioc.RQA.120.zip: Linux examples

Arioc v1.10 installation archives and source code:

AriocSetup.msi: Windows binaries and examples
Arioc.w.110.zip: Windows source code only
Arioc.x.110.zip: Linux source code
Arioc.RQA.110.zip: Linux examples

Arioc v1.04 executable binaries, examples, and source code:

AriocSetup.msi: Windows binaries and examples
Arioc.Linux.zip: Linux binaries and examples
Arioc.104.zip: source code

Removed experimental seed-coverage code from AriocP implementation.

Arioc v1.01 executable binaries and examples:

AriocSetup.msi: Windows
Arioc.Linux.zip: Linux