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alexpreynolds committed Jun 18, 2017
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Expand Up @@ -17,44 +17,44 @@ v2.4.27

Released: **TBD**

This build of BEDOPS includes significant performance improvements. Tests were performed on whole-genome TRANSFAC FIMO scans, with cache purges in between runs.
This revision of BEDOPS includes significant performance improvements for default and :code:`megarow` builds of BEDOPS. Tests were performed on whole-genome TRANSFAC FIMO scans, with cache purges in between runs.

* :ref:`bedops <bedops>`

* Performance of `bedops` tool increased by **1.3x** (or **23%**).
* Performance of :code:`bedops` tool increased by **1.3x** (or **23%**).

* Performance of `-u`/`--everything` with large numbers of inputs is improved by approximately **1.8x**.
* Performance of :code:`-u`/`--everything` with large numbers of inputs is improved by approximately **1.8x**.

* `megarow` build target is available to compile a worst-case interval-optimized version of `bedops` that preserves speed improvements at the cost of increased memory usage.
* :code:`megarow` build target is available to compile a worst-case interval-optimized version of `bedops` that preserves speed improvements at the cost of increased memory usage.

* :ref:`bedmap <bedmap>`

* Performance of `bedmap` tool increased by **1.2x** (or **15%**).
* Performance of :code:`bedmap` tool increased by **1.2x** (or **15%**).

* `megarow` build target is available to compile a worst-case interval-optimized version of `bedmap` that preserves speed improvements at the cost of increased memory usage.
* :code:`megarow` build target is available to compile a worst-case interval-optimized version of :code:`bedmap` that preserves speed improvements at the cost of increased memory usage.

* New `--min-memory` option for use when the reference file has very large regions, and the map file has many small regions that fall within those larger regions. One example is when `--range 100000` is used and the map file consists of whole-genome motif scan hits.
* New :code:`--min-memory` option for use when the reference file has very large regions, and the map file has many small regions that fall within those larger regions. One example is when :code:`--range 100000` is used and the map file consists of whole-genome motif scan hits.

* :ref:`closest-features <closest-features>`

* Performance of `closest-features` tool increased by **1.1x** (or **9%**).
* Performance of :code:`closest-features` tool increased by **1.1x** (or **9%**).

* :ref:`bam2bed <bam2bed>` and `sam2bed <sam2bed>`
* :ref:`bam2bed <bam2bed>` and :ref:`sam2bed <sam2bed>`

* Increased thread I/O heap buffer size to reduce likelihood of overflows while parsing reads from Nanopore and PacBio platforms.
* Added `--split-with-deletions` option to split spliced junctions by `N` and `D` CIGAR operations. The `--split` option now splits only on `N` operations.
* Added :code:`--split-with-deletions` option to split spliced junctions by :code:`N` and :code:`D` CIGAR operations. The :code:`--split` option now splits only on :code:`N` operations.

* :ref:`sort-bed <sort-bed>`

* Increased maximum line length to approximately 4 MB per line, to be able to sort output from converting ultra-long reads from Nanopore and PacBio platforms to BED via `convert2bed`.
* Increased maximum line length to approximately 4 MB per line, to be able to sort output from converting ultra-long reads from Nanopore and PacBio platforms to BED via :code:`convert2bed`.

* :ref:`starch <starch>`

* Fixed potential segmentation fault with `--header` usage.
* Fixed potential segmentation fault with :code:`--header` usage.

* :ref: Starch C++ API
* Starch C++ API

* Fixed output from `bedops -u` (multiset union) on two or more Starch archives, such that the remainder string was not being cleared correctly.
* Fixed output from :code:`bedops -u` (multiset union) on two or more Starch archives, such that the remainder string was not being cleared correctly.

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