From 307f634fc03b2ab24c1b3aa0a99370b517c8d104 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Wed, 24 Mar 2021 16:11:06 +0100 Subject: [PATCH 1/2] [DOC] Add changelog entry for #2458 --- CHANGELOG.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 674d43a99d..2d70f1dcb5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -96,6 +96,15 @@ If possible, provide tooling that performs the changes, e.g. a shell-script. * Requesting the alignment without also requesting the sequence for BAM files containing empty CIGAR strings does now not result in erroneous parsing ([\#2418](https://github.com/seqan/seqan3/pull/2418)). * BAM files with 64 references are now parsed correctly ([\#2423](https://github.com/seqan/seqan3/pull/2423)). +* Writing `gz`-compressed output no longer results in `bgzf`-compressed output. This change may have following effects + ([\#2458](https://github.com/seqan/seqan3/pull/2458)). + * A noticeable slowdown when writing `gz`-compressed content since, in contrast to `bgzf`, `gz` does not feature + parallelisation (magnitude depends on the application and level of parallelisation). + * A reduced output size when writing `gz`-compressed content due to `gz` storing less metadata than `bgzf` + (up to 20% smaller file size). + * The processed data should experience no negative effects since `gz` and `bgzf` are **fully compatible**. + * This bug may also cause unexpected parallelisation when reading `gz`-compressed input. This is the case when the + `gz`-compressed input was also generated with SeqAn. ## API changes @@ -174,8 +183,8 @@ If possible, provide tooling that performs the changes, e.g. a shell-script. #### Search * We removed the concepts seqan3::[bi_]fm_index[_cursor]_specialisation. We did this because we currently have only one - implementation modelling each concept and are not completely sure if the current definition of the concepts is the - right one. If you used those concepts, you can check whether the cursor type is seqan3::[bi_]fm_index_cursor as a + implementation modelling each concept and are not completely sure if the current definition of the concepts is the + right one. If you used those concepts, you can check whether the cursor type is seqan3::[bi_]fm_index_cursor as a substitute. ([\#2348](https://github.com/seqan/seqan3/pull/2348)) # 3.0.2 From 6f27c2ee095013d6a2a475d20bd781a8c1796a82 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Thu, 25 Mar 2021 16:20:25 +0100 Subject: [PATCH 2/2] Update CHANGELOG.md Co-authored-by: Lydia Buntrock --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d70f1dcb5..79fe800a4f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -97,7 +97,7 @@ If possible, provide tooling that performs the changes, e.g. a shell-script. not result in erroneous parsing ([\#2418](https://github.com/seqan/seqan3/pull/2418)). * BAM files with 64 references are now parsed correctly ([\#2423](https://github.com/seqan/seqan3/pull/2423)). * Writing `gz`-compressed output no longer results in `bgzf`-compressed output. This change may have following effects - ([\#2458](https://github.com/seqan/seqan3/pull/2458)). + ([\#2458](https://github.com/seqan/seqan3/pull/2458)): * A noticeable slowdown when writing `gz`-compressed content since, in contrast to `bgzf`, `gz` does not feature parallelisation (magnitude depends on the application and level of parallelisation). * A reduced output size when writing `gz`-compressed content due to `gz` storing less metadata than `bgzf`