[med-svn] [Git][med-team/nanoplot][master] 4 commits: New upstream version 1.30.1

Steffen Möller gitlab at salsa.debian.org
Sun Jul 5 21:14:29 BST 2020



Steffen Möller pushed to branch master at Debian Med / nanoplot


Commits:
a5721728 by Steffen Moeller at 2020-07-05T22:14:55+02:00
New upstream version 1.30.1
- - - - -
a7584c56 by Steffen Moeller at 2020-07-05T22:14:55+02:00
routine-update: New upstream version

- - - - -
20e98f2a by Steffen Moeller at 2020-07-05T22:14:55+02:00
Update upstream source from tag 'upstream/1.30.1'

Update to upstream version '1.30.1'
with Debian dir 1090cfcdbb28d865f76faaded79b72db5e73dbe4
- - - - -
612411d7 by Steffen Moeller at 2020-07-05T22:14:55+02:00
routine-update: debhelper-compat 13

- - - - -


14 changed files:

- + LICENSE
- NanoPlot.egg-info/PKG-INFO
- NanoPlot.egg-info/SOURCES.txt
- NanoPlot.egg-info/requires.txt
- PKG-INFO
- README.md
- + README.rst
- debian/changelog
- debian/control
- nanoplot/NanoPlot.py
- nanoplot/utils.py
- nanoplot/version.py
- scripts/test.sh
- setup.py


Changes:

=====================================
LICENSE
=====================================
@@ -0,0 +1,674 @@
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+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
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+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>..
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.


=====================================
NanoPlot.egg-info/PKG-INFO
=====================================
@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: NanoPlot
-Version: 1.29.0
+Version: 1.30.1
 Summary: Plotting suite for Oxford Nanopore sequencing data and alignments
 Home-page: https://github.com/wdecoster/NanoPlot
 Author: Wouter De Coster
 Author-email: decosterwouter at gmail.com
-License: MIT
+License: GPLv3
 Description: # NanoPlot
         Plotting tool for long read sequencing data and alignments.   
         
@@ -175,6 +175,8 @@ Description: # NanoPlot
         ## CITATION
         If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
         
+        Copyright: 2016-2020 Wouter De Coster <decosterwouter at gmail.com>
+        
 Keywords: nanopore sequencing plotting quality control
 Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta


=====================================
NanoPlot.egg-info/SOURCES.txt
=====================================
@@ -1,5 +1,7 @@
+LICENSE
 MANIFEST.in
 README.md
+README.rst
 setup.py
 NanoPlot.egg-info/PKG-INFO
 NanoPlot.egg-info/SOURCES.txt


=====================================
NanoPlot.egg-info/requires.txt
=====================================
@@ -4,10 +4,9 @@ pandas>=0.22.0
 numpy
 scipy
 python-dateutil
-seaborn>=0.9.0
+seaborn>=0.10.1
 matplotlib>=3.1.3
-nanoget>=1.9.0
+nanoget>=1.13.0
 nanomath>=0.23.1
-pauvre==0.1.86
-statsmodels==0.10.1
+pauvre==0.2.0
 plotly>=4.1.0


=====================================
PKG-INFO
=====================================
@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: NanoPlot
-Version: 1.29.0
+Version: 1.30.1
 Summary: Plotting suite for Oxford Nanopore sequencing data and alignments
 Home-page: https://github.com/wdecoster/NanoPlot
 Author: Wouter De Coster
 Author-email: decosterwouter at gmail.com
-License: MIT
+License: GPLv3
 Description: # NanoPlot
         Plotting tool for long read sequencing data and alignments.   
         
@@ -175,6 +175,8 @@ Description: # NanoPlot
         ## CITATION
         If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
         
+        Copyright: 2016-2020 Wouter De Coster <decosterwouter at gmail.com>
+        
 Keywords: nanopore sequencing plotting quality control
 Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta


=====================================
README.md
=====================================
@@ -166,3 +166,5 @@ Bivariate plot of mapping quality against basecall quality||||x|||dot, hex, kde
 
 ## CITATION
 If you use this tool, please consider citing our [publication](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939).
+
+Copyright: 2016-2020 Wouter De Coster <decosterwouter at gmail.com>


=====================================
README.rst
=====================================
@@ -0,0 +1,346 @@
+NanoPlot
+========
+
+Plotting tool for long read sequencing data and alignments.
+
+|Twitter URL| |conda badge| |Build Status|
+
+NanoPlot is also available as a `web service <http://nanoplot.bioinf.be>`__.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. figure:: https://github.com/wdecoster/NanoPlot/blob/master/examples/scaled_Log_Downsampled_LengthvsQualityScatterPlot_kde.png
+   :alt: Example plot
+
+   Example plot
+
+The example plot above shows a bivariate plot comparing log transformed
+read length with average basecall Phred quality score. More examples can
+be found in the `gallery on my blog ‘Gigabase Or
+Gigabyte’. <https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/>`__
+
+In addition to various plots also a NanoStats file is created
+summarizing key features of the dataset.
+
+| This script performs data extraction from Oxford Nanopore sequencing
+  data in the following formats:
+| - fastq files
+| (can be bgzip, bzip2 or gzip compressed)
+| - fastq files generated by albacore, guppy or MinKNOW containing
+  additional information
+| (can be bgzip, bzip2 or gzip compressed)
+| - sorted bam files
+| - sequencing_summary.txt output table generated by albacore, guppy or
+  MinKnow basecalling (can be gzip, bz2, zip and xz compressed) - fasta
+  files (can be bgzip, bzip2 or gzip compressed)
+| Multiple files of the same type can be offered simultaneously
+
+INSTALLATION
+~~~~~~~~~~~~
+
+``pip install NanoPlot``
+
+| Upgrade to a newer version using:
+| ``pip install NanoPlot --upgrade``
+
+or
+
+| |conda badge|
+| ``conda install -c bioconda nanoplot``
+
+The script is written for python3.
+
+OUTPUT
+~~~~~~
+
+NanoPlot creates: - a statistical summary - a number of plots - a html
+summary file
+
+USAGE
+~~~~~
+
+::
+
+   NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw]
+                   [-o OUTDIR] [-p PREFIX] [--maxlength N] [--minlength N]
+                   [--drop_outliers] [--downsample N] [--loglength]
+                   [--percentqual] [--alength] [--minqual N]
+                   [--readtype {1D,2D,1D2}] [--barcoded] [--runtime_until N]
+                   [-c COLOR]
+                   [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
+                   [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]]
+                   [--listcolors] [--no-N50] [--N50] [--title TITLE]
+                   (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --cram file [file ...] | --pickle pickle)
+
+
+   General options:
+     -h, --help            show the help and exit
+     -v, --version         Print version and exit.
+     -t, --threads THREADS Set the allowed number of threads to be used by the script
+     --verbose             Write log messages also to terminal.
+     --store               Store the extracted data in a pickle file for future plotting.
+     --raw                 Store the extracted data in tab separated file.
+     -o, --outdir OUTDIR   Specify directory in which output has to be created.
+     -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.
+
+   Options for filtering or transforming input prior to plotting:
+     --maxlength N         Hide reads longer than length specified.
+     --minlength N         Hide reads shorter than length specified.
+     --drop_outliers       Drop outlier reads with extreme long length.
+     --downsample N        Reduce dataset to N reads by random sampling.
+     --loglength           Logarithmic scaling of lengths in plots.
+     --percentqual         Use qualities as theoretical percent identities.
+     --alength             Use aligned read lengths rather than sequenced length (bam mode)
+     --minqual N           Drop reads with an average quality lower than specified.
+     --runtime_until N     Only take the N first hours of a run
+     --readtype            Which read type to extract information about from a summary file.
+                           One of 1D (default), 2D, 1D2
+     --barcoded            Use if you want to split the summary file by barcode
+
+   Options for customizing the plots created:
+     -c, --color COLOR     Specify a color for the plots, must be a valid matplotlib color
+     -f, --format          Specify the output format of the plots.
+                           One of png [default], eps,jpeg,jpg,pdf,pgf,ps,raw,rgba,svg,svgz,tif,tiff
+     --plots               Specify which bivariate plots have to be made..
+                           One or more of 'dot' (default), 'kde' (default), 'hex' and 'pauvre'
+     --listcolors          List the colors which are available for plotting and exit.
+     --no-N50              Hide the N50 mark in the read length histogram
+     --N50                 Show the N50 mark in the read length histogram
+     --title TITLE         Add a title to all plots, requires quoting if using spaces
+
+   Input data sources, one of these is required.:
+     --fastq file [file ...]
+                           Data is in one or more default fastq file(s).
+     --fasta file [file ...]
+                           Data is in one or more default fasta file(s).
+     --fastq_rich file [file ...]
+                           Data is in one or more fastq file(s) generated by albacore or MinKNOW with
+                           additional information concerning channel and time.
+     --fastq_minimal file [file ...]
+                           Data is in one or more fastq file(s) generated by albacore or MinKNOW with
+                           additional information concerning channel and time. Minimal data is extracted
+                           swiftly without elaborate checks.
+     --summary file [file ...]
+                           Data is in one or more summary file(s) generated by albacore or guppy.
+     --bam file [file ...]
+                           Data is in one or more sorted bam file(s).
+     --cram file [file ...]
+                           Data is in one or more sorted cram file(s).
+     --pickle pickle       Data is a pickle file stored earlier.
+
+NOTES
+~~~~~
+
+-  ``--downsample`` won’t save you tons of time, as down sampling is
+   only done after collecting all data and probably would only make a
+   difference for a huge amount of data. If you want to save time you
+   could down sample your data upfront. Note also that extracting
+   information from a summary file is faster than other formats, and
+   that you can extract from multiple files simultaneously (which will
+   happen in parallel then). Some plot types (especially kde) are slower
+   than others and you can take a look at the input for ``--plots`` to
+   speed things up (default is to make both kde and dot plot). If you
+   are only interested in say the read length histogram it is possible
+   to write a script to just get you that and avoid wasting time on the
+   rest. Let me know if you need any help here.
+
+EXAMPLE USAGE
+~~~~~~~~~~~~~
+
+.. code:: bash
+
+   Nanoplot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed  
+   NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot
+   NanoPlot -t 12 --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000 -o bamplots_downsampled
+
+This script now also provides read length vs mean quality plots in the
+‘`pauvre <https://github.com/conchoecia/pauvre>`__’-style from
+[@conchoecia](https://github.com/conchoecia).
+
+ACKNOWLEDGMENTS/CONTRIBUTORS
+----------------------------
+
+-  Andreas Sjödin for building and maintaining conda recipes
+-  Darrin Schultz [@conchoecia](https://github.com/conchoecia) for
+   Pauvre code
+-  [@alexomics](https://github.com/alexomics) for fixing the indentation
+   of the printed stats
+-  Botond Sipos [@bsipos](https://github.com/bsipos) for speeding up the
+   calculation of average quality scores
+
+CONTRIBUTING
+------------
+
+I welcome all suggestions, bug reports, feature requests and
+contributions. Please leave an
+`issue <https://github.com/wdecoster/NanoPlot/issues>`__ or open a pull
+request. I will usually respond within a day, or rarely within a few
+days.
+
+PLOTS GENERATED
+---------------
+
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Plot   | Fastq  | Fast   | F      | Bam    | S      | O      | Style  |
+|        |        | q_rich | astq_m |        | ummary | ptions |        |
+|        |        |        | inimal |        |        |        |        |
++========+========+========+========+========+========+========+========+
+| His    | x      | x      | x      | x      | x      | N50    |        |
+| togram |        |        |        |        |        |        |        |
+| of     |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| His    | x      | x      | x      | x      | x      | N50    |        |
+| togram |        |        |        |        |        |        |        |
+| of     |        |        |        |        |        |        |        |
+| (log   |        |        |        |        |        |        |        |
+| transf |        |        |        |        |        |        |        |
+| ormed) |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv    | x      | x      |        | x      | x      | log    | dot,   |
+| ariate |        |        |        |        |        | tr     | hex,   |
+| plot   |        |        |        |        |        | ansfor | kde,   |
+| of     |        |        |        |        |        | mation | pauvre |
+| length |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| gainst |        |        |        |        |        |        |        |
+| base   |        |        |        |        |        |        |        |
+| call   |        |        |        |        |        |        |        |
+| q      |        |        |        |        |        |        |        |
+| uality |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| H      |        | x      |        |        | x      |        |        |
+| eatmap |        |        |        |        |        |        |        |
+| of     |        |        |        |        |        |        |        |
+| reads  |        |        |        |        |        |        |        |
+| per    |        |        |        |        |        |        |        |
+| c      |        |        |        |        |        |        |        |
+| hannel |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Cumu   |        | x      | x      |        | x      |        |        |
+| lative |        |        |        |        |        |        |        |
+| yield  |        |        |        |        |        |        |        |
+| plot   |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Violin |        | x      | x      |        | x      |        |        |
+| plot   |        |        |        |        |        |        |        |
+| of     |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
+| over   |        |        |        |        |        |        |        |
+| time   |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Violin |        | x      |        |        | x      |        |        |
+| plot   |        |        |        |        |        |        |        |
+| of     |        |        |        |        |        |        |        |
+| base   |        |        |        |        |        |        |        |
+| call   |        |        |        |        |        |        |        |
+| q      |        |        |        |        |        |        |        |
+| uality |        |        |        |        |        |        |        |
+| over   |        |        |        |        |        |        |        |
+| time   |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv    |        |        |        | x      |        |        | dot,   |
+| ariate |        |        |        |        |        |        | hex,   |
+| plot   |        |        |        |        |        |        | kde    |
+| of     |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| ligned |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| gainst |        |        |        |        |        |        |        |
+| seq    |        |        |        |        |        |        |        |
+| uenced |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv    |        |        |        | x      |        | log    | dot,   |
+| ariate |        |        |        |        |        | tr     | hex,   |
+| plot   |        |        |        |        |        | ansfor | kde    |
+| of     |        |        |        |        |        | mation |        |
+| p      |        |        |        |        |        |        |        |
+| ercent |        |        |        |        |        |        |        |
+| ref    |        |        |        |        |        |        |        |
+| erence |        |        |        |        |        |        |        |
+| id     |        |        |        |        |        |        |        |
+| entity |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| gainst |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv    |        |        |        | x      |        |        | dot,   |
+| ariate |        |        |        |        |        |        | hex,   |
+| plot   |        |        |        |        |        |        | kde    |
+| of     |        |        |        |        |        |        |        |
+| p      |        |        |        |        |        |        |        |
+| ercent |        |        |        |        |        |        |        |
+| ref    |        |        |        |        |        |        |        |
+| erence |        |        |        |        |        |        |        |
+| id     |        |        |        |        |        |        |        |
+| entity |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| gainst |        |        |        |        |        |        |        |
+| base   |        |        |        |        |        |        |        |
+| call   |        |        |        |        |        |        |        |
+| q      |        |        |        |        |        |        |        |
+| uality |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv    |        |        |        | x      |        | log    | dot,   |
+| ariate |        |        |        |        |        | tr     | hex,   |
+| plot   |        |        |        |        |        | ansfor | kde    |
+| of     |        |        |        |        |        | mation |        |
+| m      |        |        |        |        |        |        |        |
+| apping |        |        |        |        |        |        |        |
+| q      |        |        |        |        |        |        |        |
+| uality |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| gainst |        |        |        |        |        |        |        |
+| read   |        |        |        |        |        |        |        |
+| length |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+| Biv    |        |        |        | x      |        |        | dot,   |
+| ariate |        |        |        |        |        |        | hex,   |
+| plot   |        |        |        |        |        |        | kde    |
+| of     |        |        |        |        |        |        |        |
+| m      |        |        |        |        |        |        |        |
+| apping |        |        |        |        |        |        |        |
+| q      |        |        |        |        |        |        |        |
+| uality |        |        |        |        |        |        |        |
+| a      |        |        |        |        |        |        |        |
+| gainst |        |        |        |        |        |        |        |
+| ba     |        |        |        |        |        |        |        |
+| secall |        |        |        |        |        |        |        |
+| q      |        |        |        |        |        |        |        |
+| uality |        |        |        |        |        |        |        |
++--------+--------+--------+--------+--------+--------+--------+--------+
+
+COMPANION SCRIPTS
+-----------------
+
+-  `NanoComp <https://github.com/wdecoster/nanocomp>`__: comparing
+   multiple runs
+-  `NanoStat <https://github.com/wdecoster/nanostat>`__: statistic
+   summary report of reads or alignments
+-  `NanoFilt <https://github.com/wdecoster/nanofilt>`__: filtering and
+   trimming of reads
+-  `NanoLyse <https://github.com/wdecoster/nanolyse>`__: removing
+   contaminant reads (e.g. lambda control DNA) from fastq
+
+CITATION
+--------
+
+If you use this tool, please consider citing our
+`publication <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty149/4934939>`__.
+
+Copyright: 2016-2020 Wouter De Coster decosterwouter at gmail.com
+
+.. |Twitter URL| image:: https://img.shields.io/twitter/url/https/twitter.com/wouter_decoster.svg?style=social&label=Follow%20%40wouter_decoster
+   :target: https://twitter.com/wouter_decoster
+.. |conda badge| image:: https://anaconda.org/bioconda/nanoplot/badges/installer/conda.svg
+   :target: https://anaconda.org/bioconda/nanoplot
+.. |Build Status| image:: https://travis-ci.org/wdecoster/NanoPlot.svg?branch=master
+   :target: https://travis-ci.org/wdecoster/NanoPlot


=====================================
debian/changelog
=====================================
@@ -1,5 +1,9 @@
-nanoplot (1.29.0-1) UNRELEASED; urgency=medium
+nanoplot (1.30.1-1) UNRELEASED; urgency=medium
 
+  [ Andreas Tille ]
   * Initial release (Closes: #<bug>)
 
+  [ Steffen Moeller ]
+  * debhelper-compat 13 (routine-update)
+
  -- Andreas Tille <tille at debian.org>  Wed, 22 Apr 2020 16:40:23 +0200


=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3,
                python3-setuptools,


=====================================
nanoplot/NanoPlot.py
=====================================
@@ -59,7 +59,8 @@ def main():
                 readtype=args.readtype,
                 combine="simple",
                 barcoded=args.barcoded,
-                huge=args.huge)
+                huge=args.huge,
+                keep_supp=not(args.no_supplementary))
         if args.store:
             pickle.dump(
                 obj=datadf,


=====================================
nanoplot/utils.py
=====================================
@@ -139,6 +139,10 @@ def get_args():
     filtering.add_argument("--barcoded",
                            help="Use if you want to split the summary file by barcode",
                            action="store_true")
+    filtering.add_argument("--no_supplementary",
+                           help="Use if you want to remove supplementary alignments",
+                           action="store_true",
+                           default=False)
     visual = parser.add_argument_group(
         title='Options for customizing the plots created')
     visual.add_argument("-c", "--color",


=====================================
nanoplot/version.py
=====================================
@@ -1 +1 @@
-__version__ = "1.29.0"
+__version__ = "1.30.1"


=====================================
scripts/test.sh
=====================================
@@ -12,6 +12,11 @@ NanoPlot --bam nanotest/alignment.bam --verbose
 echo ""
 echo ""
 echo ""
+echo "testing bam without supplementary alignments:"
+NanoPlot --bam nanotest/alignment.bam --verbose --no_supplementary
+echo ""
+echo ""
+echo ""
 echo "testing summary:"
 NanoPlot --summary nanotest/sequencing_summary.txt --loglength --verbose
 echo ""


=====================================
setup.py
=====================================
@@ -16,7 +16,7 @@ setup(
     url='https://github.com/wdecoster/NanoPlot',
     author='Wouter De Coster',
     author_email='decosterwouter at gmail.com',
-    license='MIT',
+    license='GPLv3',
     classifiers=[
         'Development Status :: 4 - Beta',
         'Intended Audience :: Science/Research',
@@ -36,12 +36,11 @@ setup(
                       'numpy',
                       'scipy',
                       'python-dateutil',
-                      'seaborn>=0.9.0',
+                      'seaborn>=0.10.1',
                       'matplotlib>=3.1.3',
-                      'nanoget>=1.9.0',
+                      'nanoget>=1.13.0',
                       'nanomath>=0.23.1',
-                      "pauvre==0.1.86",
-                      "statsmodels==0.10.1",
+                      "pauvre==0.2.0",
                       'plotly>=4.1.0',
                       ],
     package_data={'NanoPlot': []},
@@ -52,4 +51,5 @@ setup(
             'NanoPlot=nanoplot.NanoPlot:main',
         ],
     },
+    data_files=[("", ["LICENSE"])]
 )



View it on GitLab: https://salsa.debian.org/med-team/nanoplot/-/compare/d815968f256a70ca8065efcfc8fb2a83900bceee...612411d72b7ea940566fc853bb5cd47b3f85e374

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanoplot/-/compare/d815968f256a70ca8065efcfc8fb2a83900bceee...612411d72b7ea940566fc853bb5cd47b3f85e374
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