Arioc v1.52

Notes for Arioc v1.52:

The current build is v1.52.3144 (21 September 2024).

This is an interim release to address problems that have been identified and fixed since the release of v1.51.

Arioc v1.52 reference-genome lookup tables are incompatible with those generated by AriocE in release v1.43 and earlier. If you are upgrading to v1.52 from an earlier version of Arioc, please re-execute AriocE to create new lookup tables. Updated, pre-encoded lookup tables for the human, mouse, and bread yeast reference genomes are also available at ftp://ftp.ccb.jhu.edu/pub/data/Arioc, the FTP server for the Center for Computational Biology at Johns Hopkins University.

Bug fixes

• AriocE, AriocU, AriocP: fail with spurious error messages when a short reference sequence contains no nongapped seeds (see #33)
• AriocE: out-of-order @PG in SAM output
• AriocE: buffer size validation error when an aggregate FASTA file contains a very short reference sequence (see #35)
• AriocU, AriocP: error message despite valid alignment score function when read length is only a few bases longer than seed width (see #36)
• AriocU, AriocP: seed iteration error with read length < (1.5 * seed width)

Downloads

file	content
Arioc.RQA.152.zip	Linux examples
Arioc.w.152.zip	Windows source code
Arioc.x.152.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.51

Notes for Arioc v1.51:

The current build is v1.51.3140 (17 May 2023).

This is a stable, performance-tested build.

Arioc v1.51 reference-genome lookup tables are incompatible with those generated by AriocE in release v1.43 and earlier. If you are upgrading to v1.51 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://ftp.ccb.jhu.edu/pub/data/Arioc, the FTP server for the Center for Computational Biology at Johns Hopkins University.

New features

• AriocU, AriocP: increased accuracy of MAPQ computation model
• AriocU, AriocP: configuration parameter AtN is no longer supported
• AriocU, AriocP: binary output formats specific for the Terabase Search Engine (TSE, KMH) are no longer supported
• AriocU, AriocP: in repetitive regions where the placement of a short variant (SNV, indel) is arbitrary (upper track in the following image), Arioc reports the "leftmost" location within the region (lower track in the following image); this behavior is consistent with BWA and Bowtie 2 and may facilitate variant identification in repetitive regions with low coverage:
   
  
  (See also #10.)
• AriocP: increased depth-of-search in gapped alignment of mates whose opposite mate has a reportable nongapped mapping
• AriocU, AriocP: in seed-and-extend gapped alignment, added a seed-prioritization heuristic that prioritizes higher-scoring mappings for the first seeds examined; this decreases (although it does not entirely eliminate) cases where a lower-scoring but reportable mapping precludes the identification of a higher-scoring mapping associated with the last seeds examined for a read sequence.
• AriocU, AriocP: added the subRate ("substitution rate") for tuning MAPQ performance; this replaces the errorRate parameter implemented in previous Arioc versions.
• AriocU, AriocP: added the xmBQS parameter to specify a base quality score threshold for reporting methylation context for bisulfite-treated read sequences.
• AriocU, AriocP: maxJ is now a required configuration parameter.

Bug fixes

• AriocE: corrupted defline in reference sequence longer than 21 million bases in FASTA file containing multiple reference sequences (see #31).
• AriocP: incorrect alignment score (AS) reported for occasional mates aligned by Smith Waterman alignment within regions "anchored" by their mapped opposite mates.
• AriocU, AriocP: data-dependent CUDA memory access exception when lookup tables are partitioned across four or more GPU devices (useHJinGPmem="1").
• AriocE: possible error in multithreaded generation of genome configuration metadata.

Downloads

file	content
Arioc.RQA.151.zip	Linux examples
Arioc.w.151.zip	Windows source code
Arioc.x.151.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.50

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://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

Downloads

file	content
Arioc.RQA.150.zip	Linux examples
Arioc.w.150.zip	Windows source code
Arioc.x.150.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.43

Notes for Arioc v1.43:

The current build is v1.43.2994 (19 April 2021).

New features

• AriocP: added Vtw configuration parameter to relax minimum alignment score constraint on pairs where one mate is "hard to align" (see User Guide)
• AriocU, AriocP: added errorRate parameter for scaling MAPQ values (see User Guide)
• AriocU, AriocP: refined MAPQ computation model to improve compatibility with GATK HaplotypeCaller
   
  For comparison, here are some results from hap.py for whole genome sequencing of HG002 (PrecisionFDA Truth Challenge v2, "difficult-to-map regions"), GATK HaplotypeCaller v4.2.0, GIAB benchmark VCF and truthset confident regions, hard-filtered on QUAL, INFO.QD, and INFO.MQ using thresholds computed with RTG vcfeval:
   
  

Bug fixes

• AriocP, AriocU: compile-time error with CUDA SDK v11.3.

Downloads

file	content
Arioc.RQA.143.zip	Linux examples
Arioc.w.143.zip	Windows source code
Arioc.x.143.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.42

Notes for Arioc v1.42:

The current build is v1.42.2963 (30 November 2020).

New features

• AriocP: added TLEN distribution output as a space-separated list that can be copied and pasted for visualization or other analysis:
  
• AriocP: added performance metrics for TLEN skewness and fraction of discordant mappings due to out-of-range TLEN.
• AriocU, AriocP: added performance metrics for MAPQ distribution.
• AriocU, AriocP: added xmClip parameter to control inclusion/exclusion of soft-clipped read sequence regions for BS-seq methylation context mapping (SAM XM field).
• AriocU, AriocP: implemented more stringent unduplication on reported "rejected" mappings.

Bug fixes

• AriocU, AriocP: incorrect POS reported for certain reads that straddle the origin of a reference sequence with circular topology
• AriocU, AriocP: incorrect XM reported for soft-clipped reads whose highest-scoring alignments map the reverse complement of the read sequence to the reverse complement of the reference ("non-directional" BS-seq alignments)

Downloads

file	content
Arioc.RQA.142.zip	Linux examples
Arioc.w.142.zip	Windows source code
Arioc.x.142.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.41

Notes for Arioc v1.41:

The current build is v1.41.2923 (3 July 2020). This is a stable, performance-tested build.

New features

• MAPQ computed using exponentiated scores in a partition function

Bug fixes

(none)

Downloads

file	content
Arioc.RQA.141.zip	Linux examples
Arioc.w.141.zip	Windows source code
Arioc.x.141.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.40

Notes for Arioc v1.40:

The current build is v1.40.2885 (1 May 2020).

This is a stable, performance-tested build.

Arioc v1.40 is not compatible with reference-genome lookup tables generated by release v1.30 and earlier. If you are upgrading to v1.40 from v1.30 or earlier, please re-execute AriocE to create new lookup tables as documented in the User Guide.

New features

• support for NVlink GPU memory interconnect
• more efficient concurrent use of available CPU threads
• added performance metrics (CUDA compute capability verification, GPU memory utilization, file output timing)
• support for circular reference-sequence topology
• added AS (genome assembly identifier) and M5 (MD5 checksum) tags to SAM @SQ records
• revised SAM c3 (triplet complexity score) tag to use DUST weighting and phred representation
• reformatted tabular results to reconcile with output from samtools flagstat
• detailed discussion of performance tuning, including previously-undocumented extra (X) parameters for fine-grained control

Bug fixes

• AriocP, AriocU: hang (infinite loop) with certain short QNAME fields
• AriocP: failure to recognize encoded query-sequence files (*a21.sbf) with certain multi-part filenames
• AriocE: segfault when encoding reads with certain multi-part filenames
• AriocU, AriocP: segfault when aligning samples that contain widely-varying read lengths
• AriocP: data-consistency validation exception with pairs where mate 1 has multiple nongapped mappings and mate 2 is unmapped
• AriocE: spurious error message at startup when no GPU is installed
• AriocU, AriocP: failure to emit CPU description in certain Power9 Linux configurations
• AriocU: duplicate mappings in SAM file with certain large-memory hardware configurations
• AriocP: inaccurate timing of GPU-to-CPU data-transfer performance metric for nongapped mappings
• AriocP, AriocU: updated SAM NM (edit distance) computation to conform to current SAM optional fields specification

Downloads

file	content
Arioc.RQA.140.zip	Linux examples
Arioc.w.140.zip	Windows source code
Arioc.x.140.zip	Linux source code
AriocSetup.msi	Windows binaries and examples

Arioc v1.31

Notes for Arioc v1.31:

The current build is v1.31.2566 (28 June 2019).

Arioc v1.31 is not compatible with reference-genome lookup tables generated by previous versions of the software. If you are upgrading to v1.31 from an earlier release, you must re-execute AriocE to create new lookup tables as documented in the User Guide.

New features

• user-specified reference sequence names (e.g., "chr1")
• new SAM tag c3 reports the number of distinct triplets in each read sequence

Bug fixes

(none)

Downloads

AriocSetup.msi: Windows binaries and examples
Arioc.w.131.zip: Windows source code
Arioc.x.131.zip: Linux source code
Arioc.RQA.131.zip: Linux examples

Arioc v1.30

Notes for Arioc v1.30:

The current build is v1.30.2559 (6 June 2019).

This is a stable, performance-tested build.

Arioc v1.30 is not compatible with reference-genome lookup tables generated by previous versions of the software. If you are upgrading to v1.30 from an earlier release, you must re-execute AriocE to create new lookup tables as documented in the User Guide.

New features

• maximum supported genome size is now 2³⁴ base pairs (17gbp)
• GPU-accelerated hashtable sorting in AriocE
• lookup table sizes are 5-10% smaller than in previous versions of Arioc
• optional MD string formatting: "standard" (strict conformance with SAM Format specification) or "compact" (saves space by omitting placeholder zeros between mismatched symbols, but incompatible with some software tools)
• improved parsing (and faster processing) of FASTQ defline and base quality score input
• minor changes to support Visual Studio 2019

Bug fixes

• AriocP: incorrect POS reported for a read whose mapping overlaps the start of the reference genome
• AriocE: unable to merge user-specified read group IDs
• AriocP, AriocU: fully-qualified executable file path not correctly displayed
• AriocP, AriocU: workaround for memory-allocation error handling with malloc() and realloc() in certain Linux implementations
• AriocE, AriocU, AriocP: insufficient buffer space for very long input filenames
• AriocP: divide-by-zero error in MAPQ computation for very short reads (~20 bases)

Downloads

AriocSetup.msi: Windows binaries and examples
Arioc.w.130.zip: Windows source code
Arioc.x.130.zip: Linux source code
Arioc.RQA.130.zip: Linux examples

Arioc v1.25

Notes for Arioc v1.25:

The current build is v1.25.2405.18255 (12 September 2018).

New features

• improved memory management of candidate reference-genome sequences in nongapped and gapped aligners
• progress messages (including estimated time remaining)

Bug fixes

• AriocU: data-dependent memory allocation error in gapped aligner
• AriocU, AriocP: intermittent thread-synchronization error (Linux version only)
• AriocU, AriocP: intermittent failure to correctly parse all attributes in the <A> element in configuration file

Downloads

AriocSetup.msi: Windows binaries and examples
Arioc.w.125.zip: Windows source code
Arioc.x.125.zip: Linux source code
Arioc.RQA.125.zip: Linux examples