rhpvorderman/sequali issues and pull requests

#204 - Investigate the CPython limited ABI

Issue - State: open - Opened by rhpvorderman 11 days ago

#203 - Use alignment flags like samtools fastq

Issue - State: open - Opened by rhpvorderman 23 days ago

#202 - Small typo under Adapter content section

Issue - State: open - Opened by SergeWielhouwer about 1 month ago - 1 comment

#201 - Release 0.12.0

Pull Request - State: closed - Opened by rhpvorderman about 2 months ago - 1 comment

#200 - Release 0.12.0

Issue - State: closed - Opened by rhpvorderman about 2 months ago

#199 - Add support for read splitting tags

Issue - State: open - Opened by rhpvorderman about 2 months ago

#198 - Properly name percentiles in sequence length distribution

Pull Request - State: closed - Opened by rhpvorderman about 2 months ago

#197 - Add N50 and N90 as summary statistics

Issue - State: open - Opened by rhpvorderman about 2 months ago

#196 - Improvement: HiFi smrtbell adapter detection

Issue - State: open - Opened by Sebastien-Raguideau about 2 months ago - 4 comments

#195 - Fix error where missing qualities in BAM file were not properly converted

Pull Request - State: closed - Opened by rhpvorderman about 2 months ago

#194 - N50 is not a median

Issue - State: closed - Opened by Sebastien-Raguideau about 2 months ago - 8 comments

#193 - Invalid character found unclear on whitespace characters.

Issue - State: open - Opened by rhpvorderman about 2 months ago

#192 - Update UniVec database. Remove duplicates from oxford_nanopore.fasta

Pull Request - State: closed - Opened by rhpvorderman 3 months ago - 1 comment

#191 - Release 0.11.1

Issue - State: closed - Opened by rhpvorderman 3 months ago

#190 - Release 0.11.1

Pull Request - State: closed - Opened by rhpvorderman 3 months ago

#189 - Fix memory leak when creating FastqRecordArrayView

Pull Request - State: closed - Opened by rhpvorderman 3 months ago

#188 - Intermittent increased memory usage on CPython 3.12

Issue - State: closed - Opened by rhpvorderman 4 months ago - 1 comment

#187 - Release 0.11.1

Pull Request - State: closed - Opened by rhpvorderman 4 months ago - 1 comment

#186 - Release 0.11.0

Pull Request - State: closed - Opened by rhpvorderman 4 months ago

#185 - Release 0.11.0

Issue - State: closed - Opened by rhpvorderman 4 months ago

#184 - Use floor rather than round for phred scores

Pull Request - State: closed - Opened by rhpvorderman 4 months ago

#183 - Make plot ids reproducible

Pull Request - State: closed - Opened by rhpvorderman 5 months ago

#182 - Make HTML reports more reproducible.

Issue - State: closed - Opened by rhpvorderman 5 months ago - 1 comment

#181 - Add pre-commit ci

Pull Request - State: closed - Opened by rhpvorderman 5 months ago

#180 - Simplified dispatch for sequence identity functions

Pull Request - State: closed - Opened by rhpvorderman 5 months ago - 1 comment

#179 - Use clang-format and pre-commit

Pull Request - State: closed - Opened by rhpvorderman 5 months ago

#178 - Simplify GC content percentage count.

Pull Request - State: closed - Opened by rhpvorderman 5 months ago

#177 - Improve BAM nibble decoding and dispatch functions at load time.

Pull Request - State: closed - Opened by rhpvorderman 5 months ago

#176 - Add FastQC-like "judgements" on the quality of the library

Issue - State: open - Opened by rhpvorderman 5 months ago

#175 - Switch prefetching to compiler builtins, so it works on all architectures.

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#174 - "Solve" the insert size distribution in order to extrapolate the estimate.

Issue - State: open - Opened by rhpvorderman 6 months ago - 2 comments

#173 - Improve overrepresented sequence sampling so common genome repeats show up less.

Issue - State: open - Opened by rhpvorderman 6 months ago - 3 comments

#172 - Rewrite some sections of the code so that these do not require SSE2 intrinsics for speed.

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#171 - Rewrite shift-AND algorithm to enable compiler auto vectorization when GCC 14.1 becomes available.

Issue - State: open - Opened by rhpvorderman 6 months ago

#170 - Release 0.10.0

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#169 - Release 0.10.0

Issue - State: closed - Opened by rhpvorderman 6 months ago

#168 - Make overrepresented table entries a fixed size table with scrolling.

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#167 - Stage hashes to prevent in-sequence duplication to affect overrepresented sequences

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#166 - Check if sequences occur multiple times in the same read.

Issue - State: closed - Opened by rhpvorderman 6 months ago - 2 comments

#165 - Heed clang compile warnings.

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#164 - Speed up sequence identity calculation by more than 10 times using AVX2 instructions

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#163 - Calculate sequence identity using avx2 vectors

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#162 - Release 0.9.1

Issue - State: closed - Opened by rhpvorderman 6 months ago

#161 - Release 0.9.1

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#160 - Fix issue with FASTQ files without adapters causing crashes for the insert size metrics module.

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#159 - sequali crashes when no adapters are found

Issue - State: closed - Opened by Redmar-van-den-Berg 6 months ago - 3 comments

#158 - Release 0.9.0

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#157 - Release 0.9.0

Issue - State: closed - Opened by rhpvorderman 6 months ago

#156 - Fix insert size metrics array resizing and start from a smaller size

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#155 - Paired end report has the same order as single end report.

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#154 - Add common human genome repeats and illumina Poly-G

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#153 - Add very common repeats in the human genome.

Issue - State: open - Opened by rhpvorderman 6 months ago

#152 - Paired report order is hideous

Issue - State: closed - Opened by rhpvorderman 6 months ago

#151 - Add polyA and PolyG to contaminants

Issue - State: closed - Opened by rhpvorderman 6 months ago

#150 - Sequence identification in the overrepresented sequences module now uses sequence identity

Pull Request - State: closed - Opened by rhpvorderman 6 months ago

#149 - Release 0.8.0

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#148 - Fix memory leaks found by asan

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#147 - Release 0.8.0

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#146 - Release 0.8.0

Issue - State: closed - Opened by rhpvorderman 7 months ago

#145 - Add a citation file and do some slight documentation updates.

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#144 - Make insert size code look slightly nicer.

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#143 - Fix various bugs in insert size metrics.

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#142 - Cache creating the sequence index

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#141 - Calculate insert size metrics using read 1 and read 2 overlap

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#140 - Add a citation info file or chapter

Issue - State: closed - Opened by rhpvorderman 7 months ago - 2 comments

#139 - Add a paired-end mode to sequali

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#138 - What's the meaning of adapter content?

Issue - State: open - Opened by dudududu12138 7 months ago - 6 comments

#137 - Add facilities for paired-end parsing

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#136 - Prevent cache pollution by using non-temporal hints for count arrays

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#135 - Make sequali paired-end aware

Issue - State: closed - Opened by rhpvorderman 7 months ago - 1 comment

#134 - Release 0.7.1

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#133 - Release 0.7.1

Issue - State: closed - Opened by rhpvorderman 7 months ago

#132 - Explicitly test on macos-14

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#131 - Make HTML reports HTML5 compliant

Pull Request - State: closed - Opened by rhpvorderman 7 months ago

#130 - Release 0.7.0

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#129 - Release 0.7.0

Issue - State: closed - Opened by rhpvorderman 8 months ago

#128 - Improve the report with a sidebar and downloadable images

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#127 - Rewrite ascii check so the compiler can auto vectorize.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#126 - Use testc instructions for clearer code

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#125 - Enable aarch64 builds.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#124 - Check pedantic compilation works and compile for more platforms

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#123 - Use AVX2 for kmer generation.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#122 - Use dispatch rather than compiling with different instructions

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#121 - MultiQC integration improvement suggestion

Issue - State: closed - Opened by rhpvorderman 8 months ago - 7 comments

#120 - Release 0.6.0

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#119 - Release 0.6.0

Issue - State: closed - Opened by rhpvorderman 8 months ago

#118 - Add links to documentation in the html report.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#117 - Move documentation to readthedocs

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#116 - Add a readthedocs skeleton

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#115 - Add a small table with >=QXX scores to the per sequence average quality report.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#114 - Remove unused C code.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#113 - Use UUU format to use less code

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#111 - Per read quality score distribution table

Issue - State: closed - Opened by rhpvorderman 8 months ago

#108 - Add new report

Pull Request - State: closed - Opened by rhpvorderman 8 months ago

#100 - Add a meta section for the JSON report for MultiQC.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

#100 - Add a meta section for the JSON report for MultiQC.

Pull Request - State: closed - Opened by rhpvorderman 8 months ago - 1 comment

GitHub / rhpvorderman/sequali issues and pull requests