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BLD Release 0.10

Many small fixes rather than any large new features.

Full ChangeLog:

    * Fix to lock1's return value when used with paths (#68 - reopen)
    * Support _F/_R suffixes for forward/reverse in load_mocat_sample
    * samtools_sort() now accepts by={name} to sort by read name
    * Fixed bug where header was printed even when STDOUT was used
    * Fixed bug where writing interleaved FastQ to STDOUT did not work as
    expected
    * Indices created by bwa and minimap2 are now versioned
    * arg1 in external modules is no longer always treated as a path
    * Added expand_searchpath to external modules API (closes #56)
    * Fixed bug where detection of Fastq encoding was not performed on the second pair
    * Fix saving fastq sets with --subsample (issue #85)
    * Add __extra_megahit_args to assemble() (issue #86)
    * Better error message when user mis-specifies the ngless version string
    (issue #84)
    * Support NO_COLOR environment variable (issue #83)
    * Garbage collection for temporary files (issue #79)
    * Rename --search-dir to --search-path for consistency with other API
    * Fix corner case with select() producing incorrect CIGAR strings (#92)
    * Always check output file writability (#91)
    * Make paired() accept encoding argument
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luispedro committed Nov 12, 2018
1 parent 6d9a101 commit af3b5f861947eef742ad73915bdb4ba64a5b3b94
Showing with 12 additions and 9 deletions.
  1. +1 −1 ChangeLog
  2. +1 −1 NGLess/Version.hs
  3. +1 −1 README.md
  4. +9 −6 docs/sources/whatsnew.rst
@@ -1,4 +1,4 @@
Version 0.9.1+
Version 0.10.0 2018-11-12 by luispedro
* Fix to lock1's return value when used with paths (#68 - reopen)
* Support _F/_R suffixes for forward/reverse in load_mocat_sample
* samtools_sort() now accepts by={name} to sort by read name
@@ -19,7 +19,7 @@ versionStr :: String
versionStr = showVersion version

dateStr :: String
dateStr = "Unreleased (post 0.9.1)"
dateStr = "Nov 12 2018"

gitHashStr :: String
gitHashStr = $(gitHash)
@@ -26,7 +26,7 @@ If you are using NGLess, please cite:

## Example

ngless "0.9"
ngless "0.10"
input = fastq(['ctrl1.fq','ctrl2.fq','stim1.fq','stim2.fq'])
input = preprocess(input) using |read|:
read = read[5:]
@@ -2,14 +2,15 @@
What's New (History)
====================

Development version
-------------------
Version 0.10.0
--------------

Released Nov 12 2018

Bugfixes
~~~~~~~~
- Fixed bug where header was printed even when STDOUT was used
- Fix to lock1's return value when used with paths (`#68 - reopen <https://github.com/ngless-toolkit/ngless/issues/68>`__)
- Support _F/_R suffixes for forward/reverse in load_mocat_sample
- Fixed bug where writing interleaved FastQ to STDOUT did not work as expected
- Fix saving fastq sets with --subsample (issue `#85 <https://github.com/ngless-toolkit/ngless/issues/85>`__)
- Fix (hypothetical) case where the two mate files have different FastQ encodings
@@ -18,19 +19,21 @@ User-visible improvements
~~~~~~~~~~~~~~~~~~~~~~~~~

- samtools_sort() now accepts by={name} to sort by read name
- Add __extra_megahit_args to assemble() (`issue #86 <https://github.com/ngless-toolkit/ngless/issues/86>`__)
- arg1 in external modules is no longer always treated as a path
- Added expand_searchdir to external modules API (`issue #56 <https://github.com/ngless-toolkit/ngless/issues/56/>`__)
- Add __extra_megahit_args to assemble() (`issue #86 <https://github.com/ngless-toolkit/ngless/issues/86>`__)
- Support _F/_R suffixes for forward/reverse in load_mocat_sample
- Better error messages when version is mis-specified
- Support `NO_COLOR <https://no-color.org/>`__ standard: when ``NO_COLOR`` is
present in the environment, print no colours.
- Always check output file writability (`issue #91 <https://github.com/ngless-toolkit/ngless/issues/91issue )

- ``paired()`` now accepts ``encoding`` argument (it was documented to, but mis-implemented)

Internal improvements
~~~~~~~~~~~~~~~~~~~~~

- NGLess now pre-emptively garbage collects files when they are no longer needed (issue #79)
- NGLess now pre-emptively garbage collects files when they are no longer
needed (`issue #79 <https://github.com/ngless-toolkit/ngless/issues/79/>`__)

Version 0.9.1
-------------

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