SpecHLA v1.0.10

Add missing bash shebangs to scripts using source builtin by @jonasscheid

SpecHLA v1.0.9

• @jonasscheid helps build bioconda support.
• @jonasfreimuth helps format the codes and add more test examples.

Really appreciate it!

SpecHLA v1.0.8

• add pysam to long_only_env.yml
• clarify readme
• support for latest IMGT db

SpecHLA v1.0.7

• add lite conda yml file to build env for long-read-only mode
• support older gcc
• refine doc

SpecHLA v1.0.6

• add --db to denote database dir by Redmar-van-den-Berg
• Set index.sh script to exit immediately on failure by Redmar-van-den-Berg
• add --minimap_index to construct minimap2 index and reduce memory usage in mapping for long_read_typing.py
• set max depth for long_read_typing.py
• add --strand_bias_pvalue_cutoff for longshot in long_read_typing.py
• convert sam to bam in long_read_typing.py

SpecHLA v1.0.5

In long-read-only typing, the typing step can be refined by considering both alignment length and alignment identity. By balancing these two factors, we can obtain more accurate results. If the allele with the highest alignment length differs from the allele with the highest alignment identity, it indicates potential ambiguity in typing. In such cases, multiple potential types are reported. The results are stored in a result file format similar to HLA*LA for further analysis and interpretation.

SpecHLA v1.0.4

• add -l to retain tmp files
• fix the bug in read name recognition
• refine minimap2 parameter in long-read-only typing
• use python in the conda env for g-group typing
• mask low-depth region in long-read-only typing

SpecHLA v1.0.3

As suggested by bsb2014, add a module to support HLA typing from diploid assemblies. Also, some revisions in the doc.

SpecHLA v1.0.2

As @joaohccampos suggested, we added the IMGT version information to the typing results. Also, we allow users to get the most recent IMGT database for annotation.

SpecHLA v1.0.1

Generate paper results