Sierra 3.2.1

Bugfix: Change sequence validation level for drug resistance positions so it never triggers CRITICAL error.

Sierra 3.2

This version is a milestone update that we have successfully merged the Sierra-SARS2 fork with the original Sierra-HIV code base.

Major changes:

1. Alignment program has been changed from NucAmino to PostAlign. In addition to aligning FASTA sequences using MiniMap2, it introduces codon-aware alignment and positional gap score for fine-tuning the alignment result. PostAlign also supports extracting non-continuous genes from a sequence.
2. Sequence analysis has been added for Capsid (CA). In fact, the Sierra-HIV web service is now able to support whole genome alignment for HIV-1 and to generate mutation reports for PR, RT, IN, CA, gag, pol, vif, vpr, tat, rev, vpu, env and nef.
3. A FASTQ-to-CodFreq pipeline is provided as we did for Sierra-SARS2.
4. For NGS sequence analysis, Sierra-HIV is now able to generate consensus sequence based on different threshold settings.
5. Updated validation messages.

Sierra 3.1.3a1

Update HIVDB algorithm from 9.0 to 9.1.

Sierra 3.1.1

Bugfix:

Fix a bug which causes drug resistance interpretation crashed when a drug is not available by the current algorithm.

Sierra 3.1.0

New HIVDB algorithm 9.0 is released with this version! We added scores and comments for the newly FDA approved drug Cabotegravir (CAB).

Changes:

1. GraphQL interface of AlignedGeneSequence now supports a String argument targetStrain passed to node adjustedAlignedAAs and adjustedAlignedNAs. This allows to adjust sequence alignment to references other than HIV1B (HXB2 numbering), such as HIV2A and HIV2B.
2. GraphQL interface of SequenceReadsAnalysis now accepts a new Integer argument minCodonCount for specifying per-codon cutoff by number. The original argument minPrevalence is for specifying per-codon cutoff by percentage.
3. hivfacts is updated to version 2021.3. Which includes latest lists of mutation types, DRMs, unusual mutations, signature APOBEC mutations, and APOBEC-context mutations.

Sierra 3.0.7

Bugfix:

Fix a bug in resistence interpretation results that the mutation partial scores of certain positions with multiple amino acids were incorrectly showed. For example, score of AZT for RTM184IV should be -10, but it was showed as -20. However, this bug didn't affect the final resisitance scores since they are calculated by program code not affected by this bug.

Sierra 3.0.6

Bugfix:

Fix a bug that mixture mutations with more than 6 amino acids were incorrectly taken into account for drug resistance interpretation. These mutations should be ignored.

Sierra 3.0.5

Bugfix release:

Fix (deprecated) GraphQL Subtype Enum: DataFetchingException was caused because this Enum's values were incorrectly referred to Genotype instances but not plain strings.

Sierra 3.0.4-1

Bugfix: We have fixed the TSV output option which was broken for retrieving algorithm comparison data.

Sierra 3.0.4

Bugfixes:

1. #27: Local NucAmino was referred to an old, incompatible version. This issue didn't affected HIVDB production website (hivdb.stanford.edu).
2. When drug resistance interpretation contains dosage (drug-level) comment(s), GraphQL querying "BoundComment/triggeredAAs" resulted a NullPointerException. Instead, Sierra should be able to handle this exception and returns a null value.