diff --git a/CHANGELOG.md b/CHANGELOG.md index 6e1298d..638fdc6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [v0.2.7] +### Fixes +- [dmr] Header was incorrect with multiple samples +- [pileup] Improve performance when using `--include-bed`, only process contigs in the BED file. +- [dmr, single-site] When using multiple samples, don't fail a position when one or more samples doesn't have a modification call at that position. +- [extract] Expose queue size to reduce memory usage with long reads. +- [validate] Report number of calls filtered out with thresholds. + + ## [v0.2.6] ### Fixes - [dmr, single-site] Don't require that there are equal numbers of samples for single site DMR with multiple samples. Fixes #140. diff --git a/docs/intro_dmr.html b/docs/intro_dmr.html index b848847..f32be32 100644 --- a/docs/intro_dmr.html +++ b/docs/intro_dmr.html @@ -342,12 +342,16 @@
modkit extract
.Transforming reads into a table with modkit extract
can produce large files (especially with long reads).
+Before the data can be written to disk, however, it is enqueued in memory and can potentially create a large memory burden.
+There are a few ways to decrease the amount of memory modkit extract
will use in these cases:
--queue-size
, this decreased the number of batches that will be held in flight.--ignore-index
this will force modkit extract
to run a serial scan of the mod-BAM.--interval-size
, this will decrease the size of the batches.modkit extract
.Transforming reads into a table with modkit extract
can produce large files (especially with long reads).
+Before the data can be written to disk, however, it is enqueued in memory and can potentially create a large memory burden.
+There are a few ways to decrease the amount of memory modkit extract
will use in these cases:
--queue-size
, this decreased the number of batches that will be held in flight.--ignore-index
this will force modkit extract
to run a serial scan of the mod-BAM.--interval-size
, this will decrease the size of the batches.