update README; add license

PacificBiosciences · Nov 30, 2023 · 3fd6fc4 · 3fd6fc4
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -0,0 +1,34 @@
+Copyright (c) 2023, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the
+disclaimer below) provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+
+ * Neither the name of Pacific Biosciences nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -4,11 +4,8 @@
 
 An HLA star-calling tool for PacBio HiFi data types.  
 
-IPD-IMGT/HLA Version: 3.53 (July 7, 2023)[1]
-
 Authors: [John Harting](https://github.com/jrharting), [Zev Kronenberg](https://github.com/zeeev), [Daniel Baker](https://github.com/dnbaker), [Matt Holt](https://github.com/holtjma)
 
-
 ## Table of Contents ##
 1. [Install](#install)
 2. [Genes](#genes)
@@ -20,8 +17,16 @@ Authors: [John Harting](https://github.com/jrharting), [Zev Kronenberg](https://
 
 ## Install <a name="install"></a>
 
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/hifihla/README.html)
+
 Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda) for information on Installation, Support, License, Copyright, and Disclaimer.
 
+`hifihla` can be installed from bioconda
+```
+conda install -c bioconda hifihla
+```
+Binaries are also availible in the github releases.
+
 ## Genes <a name="genes"></a>
 
 Genes called by `hifihla`:
@@ -87,26 +92,27 @@ Options:
 
 
 ### Type HLA from MHC assembled contigs
-`call-contigs` requires three input files and an output directory:
+`call-contigs` requires 2 or 3 input files and an output directory:
  * Assembled contigs aligned to GRCH38 (no alts)
- * Assembled haplotype fasta[.gz] files (2)  
+ * Assembled haplotype fasta[.gz] files (1 or 2)  
 
 Options:
+ * `hap2` is optional -- the fasta argument to `hap1` may contain one or two MHC haplotig sets.  If `hap2` is not set, alleles will be phased by contig name.
  * Define the loci to be extracted and called (see [IMGT genes](https://hla.alleles.org/genes/index.html)) [default all loci]
  * Limit equivalent matches in report -- This is useful to limit reporting of common alleles with shared cDNA.
  * Require assembly alleles to be of a minimum length
 ```
 Extract HLA loci from assembled MHC contigs & call star alleles on extracted sequences
 
-Usage: hifihla call-contigs [OPTIONS] --abam <ALIGNED_ASSEMBLY> --hap1 <HAP1_FA> --hap2 <HAP2_FA> --outdir <OUTDIR>
+Usage: hifihla call-contigs [OPTIONS] --abam <ALIGNED_ASSEMBLY> --hap1 <HAP1_FA> --outdir <OUTDIR>
 
 Options:
   -a, --abam <ALIGNED_ASSEMBLY>  Input assembly aligned to GRCh38
   -p, --hap1 <HAP1_FA>           Input hap1 assembly fa(.gz)
-  -m, --hap2 <HAP2_FA>           Input hap2 assembly fa(.gz)
+  -m, --hap2 <HAP2_FA>           Input hap2 assembly fa(.gz) (optional)
   -o, --outdir <OUTDIR>          Output directory
   -l, --loci [<LOCI>...]         Input comma-sep loci to extract [default: all]
-  -s, --min_length <MINLENGTH>   Minimum length of extracted targets [default: 2000]
+  -s, --min_length <MINLENGTH>   Minimum length of extracted targets [default: 1000]
   -x, --max_matches <MATCHES>    Maximum equivalent matches per query in report [default: 10]
   -j, --threads <THREADS>        Analysis threads [default: 1]
   -v, --verbose...               Enable verbose output
@@ -118,6 +124,10 @@ Options:
                                   -vvv => "Trace" [default: Warn]
   -h, --help                     Print help
   -V, --version                  Print version
+
+Copyright (C) 2004-2023     Pacific Biosciences of California, Inc.
+This program comes with ABSOLUTELY NO WARRANTY; it is intended for
+Research Use Only and not for use in diagnostic procedures.
 ```
 
 ### Align queries to specific alleles in IPD-IMGT/HLA
@@ -349,7 +359,7 @@ $ hifihla align-imgt \
           --fasta HG001_HLA_A_11_01_01_01.fasta \
           -n HLA-A*11:01:01:03 \
           -t HLA00043
-{                                                                                                                                              [38/1857]
+{
   "id": "Query HLA-A_11-01-01-01; Targets HLA00043,HLA15502",
   "hla_alignments": {
     "HLA-A_11-01-01-01": {
@@ -384,7 +394,7 @@ $ hifihla align-imgt \
         "noncode_eddist": 0,
         "differences": []
       },
-     "HLA15502": {                                                                                                                             [3/1857]
+     "HLA15502": {
         "allele_id": "HLA15502",
         "star_name": "HLA-A*11:01:01:03",
         "length": 3503,
@@ -440,8 +450,19 @@ Changelog - PacBio HiFi HLA Typing - hifihla
 - Latest database version v3.53
 - Bug fixes
 
+## v0.2.1: 11/15/23
+### Changes
+- Call-contigs hap2 change to optional
+- Improve output determinism
+- Update README 
+- Fix validation bugs
+
+## v0.2.2: 11/17/23
+### Changes
+- Update database to IPD-IMGT/HLA Version: 3.54 (2023-10)
+
 ## References <a name="references"></a>
-[1]: Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh SGE. _The IPD-IMGT/HLA Database_. Nucleic Acids Research (2023) 51:D1053-60.
+Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh SGE. _The IPD-IMGT/HLA Database_. Nucleic Acids Research (2023) 51:D1053-60.
 
 ## DISCLAIMER
 THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.