From 0d2ab586c76fcbd08157113815920183fb02432f Mon Sep 17 00:00:00 2001 From: rfm-targa Date: Wed, 21 Feb 2024 17:36:22 +0000 Subject: [PATCH] Updated the Readme and Changelog. --- CHANGELOG.md | 8 ++++++-- README.md | 8 ++++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b55d22fd..5c8ac9db 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,11 +10,15 @@ - Updated the Dockerfile to install chewBBACA with `python3 -m pip install .` instead of the deprecated `python setup.py install` command. -- Removed FASTA header integer conversion before running BLASTp. This was done to avoid a warning from BLAST related to sequence identifier length exceeding 50 characters. +- Removed FASTA header integer conversion before running BLASTp. This was done to avoid a warning from BLAST related to sequence header length exceeding 50 characters. - The seqids and coordinates of the CDSs closest to contig tips are stored in a dictionary during gene prediction to simplify LOTSC and PLOT5/3 determination (in many cases this reduces runtime by ~20%). -- Limited the number of values stored in memory while creating the `results_contigsInfo.tsv` output file. +- Limited the number of values stored in memory while creating the `results_contigsInfo.tsv` and `results_alleles.tsv` output files to reduce memory usage. + +- Adding data to the FASTA and TSV files for the missing classes per locus instead of storing the complete per input data to reduce memory usage. + +- The data for novel alleles is saved to files to reduce memory usage. - Fixed the in-frame stop codon count values displayed in the reports created by the SchemaEvaluator module. diff --git a/README.md b/README.md index 51a86381..e1e38d9a 100644 --- a/README.md +++ b/README.md @@ -31,11 +31,15 @@ settings and a set of functions to visualize and validate allele variation in th - Updated the Dockerfile to install chewBBACA with `python3 -m pip install .` instead of the deprecated `python setup.py install` command. -- Removed FASTA header integer conversion before running BLASTp. This was done to avoid a warning from BLAST related to sequence identifier length exceeding 50 characters. +- Removed FASTA header integer conversion before running BLASTp. This was done to avoid a warning from BLAST related to sequence header length exceeding 50 characters. - The seqids and coordinates of the CDSs closest to contig tips are stored in a dictionary during gene prediction to simplify LOTSC and PLOT5/3 determination (in many cases this reduces runtime by ~20%). -- Limited the number of values stored in memory while creating the `results_contigsInfo.tsv` output file. +- Limited the number of values stored in memory while creating the `results_contigsInfo.tsv` and `results_alleles.tsv` output files to reduce memory usage. + +- Adding data to the FASTA and TSV files for the missing classes per locus instead of storing the complete per input data to reduce memory usage. + +- The data for novel alleles is saved to files to reduce memory usage. - Fixed the in-frame stop codon count values displayed in the reports created by the SchemaEvaluator module.