Sierra 3.2.11

• Bugfix #34: Fix missing genotype results prevents Capsid analysis results.
• The leading and trailing N's are now trimmed from the input sequence for better robustness.

Sierra 3.2.10

Bugfix:

In PostAlign, avoid penalizing gaps post/pre each end of input sequence.

Sierra 3.2.9.1

Bump PostAlign to latest version to avoid an infinite loop error.

Sierra 3.2.9

Bugfixes:

1. A regression bug that prevent mutationsByTypes reporting mixtures.
2. PostAlign caused a missing gene serious warning ("Alignment of gene XX is discarded since the List of 'alignedSites' is empty or contains only gaps") by not filtering out all empty genes. This behavior has been changed and this kind of warnings will be no long reported.
3. An incorrectly concatenated (e.g. RT + PR) sequence would cause excess number of artifact mutations being reported due to the way PostAlign dealing with unaligned sequences. This issue has been resolved.

Improvement:

IUPAC simple nucleotide score is added to PostAlign's gap placement algorithm for considering both NA and AA when doing placements. For certain extreme case this hybrid score calculation generates better results than just use BLOSUM62.

Sierra 3.2.8

Bugfixes:

1. Earlier version of Sierra-HIV failed to report gene sequences that have been aligned but were dropped by Sierra due to quality reasons. We added this feature back.
2. We introduced a new concept "conditionally unsequenced regions" for flagging a mutation that closes to the boundary of a definitive unsequenced region, or belongs to a long-stretch (≥20 AAs) range deletion. These "gray area" mutations are no longer reported by the program. Instead, they are now reported as part of unsequenced regions.
3. An alignment extension algorithm is introduced to extend MiniMap2 alignment to include unaligned boundary nucleotides (hivdb/postalign).
4. MiniMap2 alignment options have been changed from "-w 5 -B 1" to "-w 5" to address certain misalignment issue. The "-B 1" was added to partially reduced the unaligned boundary nucleotides issue previously - we now have a more sophisticated algorithm doing it.

Sierra 3.2.7

Bugfix: Fix StrainModifier for handling sequence chunking.

Sierra 3.2.6

The item 1 of Sierra 3.1.0 was accidentally removed previous. This version added it back.

Sierra 3.2.4

Bugfix: Fixed the pretty pair-wise view and subtype distance for sequences that in reverse compliment.

Sierra 3.2.3

Bugfix:

Previously, a default k-mer window size=10 was applied when aligning an HIV-1 sequence by minimap2. This default window size is changed to 5 to achieve higher sensitivity for short sequences (e.g. PR only).

Sierra 3.2.2

The default behavior of includedGenes for HIV-1 is changed back to only query results for PR, RT, and IN. Explict specification is required for querying other genes.