Commit b69c70cd authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.2.13.2

parent 10673661

CHANGES.md

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# Changelog





## [1.2.13.2] - 2018-04-22

### Fixed

  - Additional fixes to divisions by zeros in summary calculations.

  - Fixed 'empty file' message if FASTA file ends with empty sequence.

  - Renamed pre-trimmed FASTQ validation/statistics file, to avoid failure if

    an older run was resumed.





## [1.2.13.1] - 2018-03-25

### Fixed 

  - Fixed divisions by zero if empty files are listed as pre-trimmed reads.





## [1.2.13] - 2018-03-25

### Added

  - Added 'retable' command for pretty-printing whitespace separated data in

    the previously used by the BAM pipeline.

  - Basic statistics are collected for pre-trimmed reads in the BAM pipeline.



### Changed

  - BAM pipeline tables are now saved as tab separated columns. The old

    pretty-printed format may be produced by running the 'retable' tool on

    the resulting files.

  - Memory usage for the 'coverage' and 'depths' commands were reduced when

    using very big BED files.



### Fixed

  - Fixed input / output files not being listed in 'pipe.errors' files.

  - Use the same max open files limit for picard (ulimit -n minus headroom)

    when determining if the default should be changed and as the final value.

  - Removed explicit test for JRE version, which was failing on some (valid)

    runtimes. Java programs are still checked prior to running pipelines.

  - Fixed changes to recent version of Pysam breaking the alignment step

    in the BAM pipeline.

  - Fixed various test failures resulting in different environments.

  - Fixed validation of pre-trimmed FASTQ files in BAM pipelines stopping

    early if empty files are encountered.



### Removed

  - Removed automatic migrating of configuration files created PALEOMIX

    PALEOMIX prior to v1.2.0.

  - Previously deprecated support for existing BAM files was removed from

    the BAM pipeline.





## [1.2.12] - 2017-08-13

### Fixed

  - Fixed input / output files not being listed in 'pipe.errors' files.
@@ -529,7 +575,10 @@ the (partially) updated documentation now hosted on ReadTheDocs. 
  - Switching to more traditional version-number tracking.





[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.12...HEAD

[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...HEAD

[1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2

[1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1

[1.2.13]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.12...v1.2.13

[1.2.12]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.11...v1.2.12

[1.2.11]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.10...v1.2.11

[1.2.10]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.9...v1.2.10

MANIFEST.in

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@@ -2,8 +2,8 @@ include README.rst 
include CHANGES.md

include MANIFEST.in

include pylint.conf

licenses/gpl.txt

licenses/mit.txt

include licenses/gpl.txt

include licenses/mit.txt

include paleomix/yaml/CHANGES

include paleomix/yaml/LICENSE

include paleomix/yaml/PKG-INFO

README.rst

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@@ -6,7 +6,7 @@ The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapi 


The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.



For a detailed description of the pipeline, please refer to `PALEOMIX <http://geogenetics.ku.dk/publications/paleomix>`_ website and the `documentation <http://paleomix.readthedocs.io/>`_; for questions, bug reports, and/or suggestions, use the `GitHub tracker <https://github.com/MikkelSchubert/paleomix/issues/>`_, or contact Mikkel Schubert at `MSchubert@snm.ku.dk <mailto:MSchubert@snm.ku.dk>`_.

For a detailed description of the pipeline, please refer to `PALEOMIX <http://geogenetics.ku.dk/publications/paleomix>`_ website and the `documentation <http://paleomix.readthedocs.io/>`_; for questions, bug reports, and/or suggestions, use the `GitHub tracker <https://github.com/MikkelSchubert/paleomix/issues/>`_, or contact Mikkel Schubert at `MikkelSch@gmail.com <mailto:MikkelSch@gmail.com>`_.



The PALEOMIX pipelines have been published in Nature Protocols; if you make use of PALEOMIX in your work, then please cite

bin/bam_pipeline

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#!/usr/bin/env python

# -*- coding: utf-8 -*-

# Copyright (c) 2014 Mikkel Schubert <MSchubert@snm.ku.dk>

# Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com>

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal

bin/bam_rmdup_collapsed

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#!/usr/bin/env python

# -*- coding: utf-8 -*-

# Copyright (c) 2014 Mikkel Schubert <MSchubert@snm.ku.dk>

# Copyright (c) 2014 Mikkel Schubert <MikkelSch@gmail.com>

#

# Permission is hereby granted, free of charge, to any person obtaining a copy

# of this software and associated documentation files (the "Software"), to deal