[med-svn] [Git][med-team/ivar][master] 5 commits: Exclude *.js, install docs
Andreas Tille
gitlab at salsa.debian.org
Wed May 13 13:28:45 BST 2020
Andreas Tille pushed to branch master at Debian Med / ivar
Commits:
6feee456 by Andreas Tille at 2020-05-13T13:56:40+02:00
Exclude *.js, install docs
- - - - -
bfa1b2ff by Andreas Tille at 2020-05-13T13:57:05+02:00
New upstream version 1.2.2+dfsg
- - - - -
cb7b5a15 by Andreas Tille at 2020-05-13T13:57:06+02:00
Update upstream source from tag 'upstream/1.2.2+dfsg'
Update to upstream version '1.2.2+dfsg'
with Debian dir 42e81a71e246ae318cadb5e749899262830d6ba4
- - - - -
8b89fc6a by Andreas Tille at 2020-05-13T14:26:59+02:00
provide link to jquery.js
- - - - -
1a6ae93a by Andreas Tille at 2020-05-13T14:28:05+02:00
Fix copyright
- - - - -
15 changed files:
- − .github/ISSUE_TEMPLATE/bug_report.md
- − .github/ISSUE_TEMPLATE/feature_request.md
- − .github/workflows/ccpp.yml
- − .gitignore
- debian/changelog
- debian/control
- debian/copyright
- + debian/ivar-doc.install
- + debian/ivar-doc.links
- + debian/ivar.docs
- + debian/source/lintian-overrides
- debian/watch
- − docs/html/jquery.js
- − docs/latex/classsuffix__node.tex.tmp
- − docs/latex/ivar_8cpp.tex.tmp
Changes:
=====================================
.github/ISSUE_TEMPLATE/bug_report.md deleted
=====================================
@@ -1,35 +0,0 @@
----
-name: Bug report
-about: Create a report to help us improve
-
----
-
-**Describe the bug**
-A clear and concise description of what the bug is.
-
-**To Reproduce**
-Steps to reproduce the behavior:
-1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
-4. See error
-
-**Expected behavior**
-A clear and concise description of what you expected to happen.
-
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
-
-**Desktop (please complete the following information):**
- - OS: [e.g. iOS]
- - Browser [e.g. chrome, safari]
- - Version [e.g. 22]
-
-**Smartphone (please complete the following information):**
- - Device: [e.g. iPhone6]
- - OS: [e.g. iOS8.1]
- - Browser [e.g. stock browser, safari]
- - Version [e.g. 22]
-
-**Additional context**
-Add any other context about the problem here.
=====================================
.github/ISSUE_TEMPLATE/feature_request.md deleted
=====================================
@@ -1,17 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for this project
-
----
-
-**Is your feature request related to a problem? Please describe.**
-A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
-
-**Describe the solution you'd like**
-A clear and concise description of what you want to happen.
-
-**Describe alternatives you've considered**
-A clear and concise description of any alternative solutions or features you've considered.
-
-**Additional context**
-Add any other context or screenshots about the feature request here.
=====================================
.github/workflows/ccpp.yml deleted
=====================================
@@ -1,85 +0,0 @@
-name: C/C++ CI
-
-on:
- push:
- branches: [ master ]
- pull_request:
- branches: [ master ]
-
-jobs:
- build-linux:
-
- runs-on: ${{ matrix.os }}
-
- strategy:
- matrix:
- os: [ubuntu-16.04, ubuntu-18.04]
-
- steps:
- - uses: actions/checkout at master
- - name: download htslib
- run: wget https://github.com/samtools/htslib/archive/1.10.2.tar.gz
- - name: untar
- run: tar xf 1.10.2.tar.gz
- - name: install htslib
- env:
- CC: gcc-7
- run: |
- cd htslib-1.10.2/
- autoheader
- autoconf
- ./configure
- make
- sudo make install
- sudo ldconfig
- - name: autotools
- env:
- CC: gcc-7
- run: ./autogen.sh
- - name: configure
- env:
- CC: gcc-7
- run: ./configure
- - name: make
- env:
- CC: gcc-7
- run: make
- - name: make check
- env:
- CC: gcc-7
- run: make check
- - name: make install
- env:
- CC: gcc-7
- run: sudo make install
-
- build-macos:
-
- runs-on: [ macos-latest ]
-
- steps:
- - uses: actions/checkout at master
- - name: install GNU autotools
- run: brew install autoconf automake libtool
- - name: download htslib
- run: wget https://github.com/samtools/htslib/archive/1.10.2.tar.gz
- - name: untar
- run: tar xf 1.10.2.tar.gz
- - name: install htslib
- run: |
- cd htslib-1.10.2/
- autoheader
- autoconf
- ./configure
- make
- sudo make install
- - name: autoconf
- run: ./autogen.sh
- - name: configure
- run: ./configure
- - name: make
- run: make
- - name: make check
- run: make check
- - name: make install
- run: sudo make install
=====================================
.gitignore deleted
=====================================
@@ -1,13 +0,0 @@
-*~
-.DS_Store
-trim_primer_quality
-**/.snakemake/*
-GPATH
-GRTAGS
-GTAGS
-*.pyc
-**/.dSYM/*
-.dSYM/*
-**/.deps/*
-**/*.o
-Makefile
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-ivar (1.2.2-1) UNRELEASED; urgency=medium
+ivar (1.2.2+dfsg-1) UNRELEASED; urgency=medium
* Initial release (Closes: #<bug>)
=====================================
debian/control
=====================================
@@ -28,3 +28,25 @@ Description: functions broadly useful for viral amplicon-based sequencing
3. variant calling - both iSNVs and insertions/deletions, and
4. identifying mismatches to primer sequences and excluding the
corresponding reads from alignment files.
+
+Package: ivar-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+ node-jquery
+Description: functions broadly useful for viral amplicon-based sequencing (documentation)
+ iVar is a computational package that contains functions broadly useful
+ for viral amplicon-based sequencing. Additional tools for metagenomic
+ sequencing are actively being incorporated into iVar. While each of
+ these functions can be accomplished using existing tools, iVar contains
+ an intersection of functionality from multiple tools that are required
+ to call iSNVs and consensus sequences from viral sequencing data across
+ multiple replicates. iVar provided the following functions:
+ .
+ 1. trimming of primers and low-quality bases,
+ 2. consensus calling,
+ 3. variant calling - both iSNVs and insertions/deletions, and
+ 4. identifying mismatches to primer sequences and excluding the
+ corresponding reads from alignment files.
+ .
+ This package contains the html documentation for ivar.
=====================================
debian/copyright
=====================================
@@ -1,11 +1,34 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: ivar
Source: https://github.com/andersen-lab/ivar/releases
+Files-Excluded: */jquery.js
+ */*.tmp
+ */.github
+ */.gitignore
Files: *
-Copyright: 20xx-20yy <upstream>
+Copyright: 2018-2020 Nathan D. Grubaugh, Karthik Gangavarapu
License: GPL-3+
+Files: docs/html/search/search.js
+ docs/html/menu.js
+ docs/html/dynsections.js
+ docs/html/menudata.js
+Copyright: 1997-2017 by Dimitri van Heesch
+License: GPL-2+
+ 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 2 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.
+ .
+ On Debian systems you can find the full text of the GNU General Public
+ License version 3 at /usr/share/common-licenses/GPL-2.
+
Files: debian/*
Copyright: 2020 Andreas Tille <tille at debian.org>
License: GPL-3+
=====================================
debian/ivar-doc.install
=====================================
@@ -0,0 +1 @@
+docs/html usr/share/doc/ivar
=====================================
debian/ivar-doc.links
=====================================
@@ -0,0 +1 @@
+usr/share/nodejs/jquery/dist/jquery.js usr/share/doc/ivar/html/jquery.js
=====================================
debian/ivar.docs
=====================================
@@ -0,0 +1,2 @@
+docs/COOKBOOK.md
+docs/MANUAL.md
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# False positive
+ivar source: source-is-missing docs/html/menu.js line length is 695 characters (>512)
+
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
https://github.com/andersen-lab/ivar/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
=====================================
docs/html/jquery.js deleted
=====================================
The diff for this file was not included because it is too large.
=====================================
docs/latex/classsuffix__node.tex.tmp deleted
=====================================
@@ -1,78 +0,0 @@
-\hypertarget{classsuffix__node}{}\section{suffix\+\_\+node Class Reference}
-\label{classsuffix__node}\index{suffix\+\_\+node@{suffix\+\_\+node}}
-
-
-Collaboration diagram for suffix\+\_\+node\+:
-% FIG 0
-\subsection*{Public Member Functions}
-\begin{DoxyCompactItemize}
-\item
-\mbox{\Hypertarget{classsuffix__node_a8622127d06af65bd3d16ce5958995b1b}\label{classsuffix__node_a8622127d06af65bd3d16ce5958995b1b}}
-{\bfseries suffix\+\_\+node} (int b, int $\ast$e, \mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$p, \mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$l)
-\item
-\mbox{\Hypertarget{classsuffix__node_ab465cab427de4e42b7b917e738b43425}\label{classsuffix__node_ab465cab427de4e42b7b917e738b43425}}
-bool {\bfseries is\+\_\+leaf\+\_\+node} ()
-\item
-\mbox{\Hypertarget{classsuffix__node_af00dced817833c98c331293ebe819de5}\label{classsuffix__node_af00dced817833c98c331293ebe819de5}}
-bool {\bfseries contains\+\_\+child} (int ext)
-\item
-\mbox{\Hypertarget{classsuffix__node_a7b47f09cf1d6a59849dba9fbcb1f3f61}\label{classsuffix__node_a7b47f09cf1d6a59849dba9fbcb1f3f61}}
-int {\bfseries get\+\_\+length} ()
-\item
-\mbox{\Hypertarget{classsuffix__node_a7fb5c818a596880ac914780e1b8c198f}\label{classsuffix__node_a7fb5c818a596880ac914780e1b8c198f}}
-int {\bfseries get\+\_\+depth} ()
-\item
-\mbox{\Hypertarget{classsuffix__node_a5469454f507f118785f65f206b141c3d}\label{classsuffix__node_a5469454f507f118785f65f206b141c3d}}
-std\+::string {\bfseries get\+\_\+longest\+\_\+common\+\_\+substring} (std\+::string s1, std\+::string s2)
-\item
-\mbox{\Hypertarget{classsuffix__node_aec052c5cffdd951390cdfb40c360908e}\label{classsuffix__node_aec052c5cffdd951390cdfb40c360908e}}
-std\+::string {\bfseries get\+\_\+path} (std\+::string s)
-\item
-\mbox{\Hypertarget{classsuffix__node_a48933a8d9a3958c56dbbe98ae43deb84}\label{classsuffix__node_a48933a8d9a3958c56dbbe98ae43deb84}}
-void {\bfseries extend\+\_\+path} (int $\ast$e)
-\item
-\mbox{\Hypertarget{classsuffix__node_af1c5aa14ccae896455815cd4c5a4d1a8}\label{classsuffix__node_af1c5aa14ccae896455815cd4c5a4d1a8}}
-\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries add\+\_\+child} (int ext, int b, int $\ast$e, \mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$l)
-\item
-\mbox{\Hypertarget{classsuffix__node_ac25245d1931525b91678167fe07c4eb7}\label{classsuffix__node_ac25245d1931525b91678167fe07c4eb7}}
-void {\bfseries add\+\_\+child} (\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$c, int ext)
-\item
-\mbox{\Hypertarget{classsuffix__node_a1ce4cfd4bf2136222a1162dd2555e2d3}\label{classsuffix__node_a1ce4cfd4bf2136222a1162dd2555e2d3}}
-\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries get\+\_\+child} (int ext)
-\item
-\mbox{\Hypertarget{classsuffix__node_a50ab619252f0ad2091337bbf9688f9bf}\label{classsuffix__node_a50ab619252f0ad2091337bbf9688f9bf}}
-bool {\bfseries contains\+\_\+depth} (int depth)
-\item
-\mbox{\Hypertarget{classsuffix__node_a050ba7b3d5859d1dafb053e34a16663b}\label{classsuffix__node_a050ba7b3d5859d1dafb053e34a16663b}}
-void {\bfseries print} (std\+::string s)
-\item
-\mbox{\Hypertarget{classsuffix__node_a931f49a361496b16bfa52609ae82630d}\label{classsuffix__node_a931f49a361496b16bfa52609ae82630d}}
-bool {\bfseries walk\+\_\+next} (int \&beg, int \&suffix\+\_\+length)
-\end{DoxyCompactItemize}
-\subsection*{Public Attributes}
-\begin{DoxyCompactItemize}
-\item
-\mbox{\Hypertarget{classsuffix__node_a9de4356329d9fd07511bcc4ee080df50}\label{classsuffix__node_a9de4356329d9fd07511bcc4ee080df50}}
-int {\bfseries begin}
-\item
-\mbox{\Hypertarget{classsuffix__node_a52e5a4ab12e08966e38db512ed6316dc}\label{classsuffix__node_a52e5a4ab12e08966e38db512ed6316dc}}
-int {\bfseries nchildren}
-\item
-\mbox{\Hypertarget{classsuffix__node_af3d0857764f653e1a0f622af5215a4a0}\label{classsuffix__node_af3d0857764f653e1a0f622af5215a4a0}}
-int $\ast$ {\bfseries end}
-\item
-\mbox{\Hypertarget{classsuffix__node_ac60ca6423a4769832874c1a6efe3d1c1}\label{classsuffix__node_ac60ca6423a4769832874c1a6efe3d1c1}}
-\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$$\ast$ {\bfseries children}
-\item
-\mbox{\Hypertarget{classsuffix__node_a3034292aaf83597ce658f45438c89133}\label{classsuffix__node_a3034292aaf83597ce658f45438c89133}}
-\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries parent}
-\item
-\mbox{\Hypertarget{classsuffix__node_a7d19dcd69e8b91ecbde055f7c4d86048}\label{classsuffix__node_a7d19dcd69e8b91ecbde055f7c4d86048}}
-\mbox{\hyperlink{classsuffix__node}{suffix\+\_\+node}} $\ast$ {\bfseries suffix\+\_\+link}
-\end{DoxyCompactItemize}
-
-
-The documentation for this class was generated from the following files\+:\begin{DoxyCompactItemize}
-\item
-src/suffix\+\_\+tree.\+h\item
-src/suffix\+\_\+tree.\+cpp\end{DoxyCompactItemize}
=====================================
docs/latex/ivar_8cpp.tex.tmp deleted
=====================================
@@ -1,67 +0,0 @@
-\hypertarget{ivar_8cpp}{}\section{src/ivar.cpp File Reference}
-\label{ivar_8cpp}\index{src/ivar.\+cpp@{src/ivar.\+cpp}}
-{\ttfamily \#include $<$iostream$>$}\newline
-{\ttfamily \#include $<$unistd.\+h$>$}\newline
-{\ttfamily \#include \char`\"{}remove\+\_\+reads\+\_\+from\+\_\+amplicon.\+h\char`\"{}}\newline
-{\ttfamily \#include \char`\"{}call\+\_\+consensus\+\_\+pileup.\+h\char`\"{}}\newline
-{\ttfamily \#include \char`\"{}call\+\_\+variants.\+h\char`\"{}}\newline
-{\ttfamily \#include \char`\"{}trim\+\_\+primer\+\_\+quality.\+h\char`\"{}}\newline
-{\ttfamily \#include \char`\"{}get\+\_\+masked\+\_\+amplicons.\+h\char`\"{}}\newline
-{\ttfamily \#include \char`\"{}suffix\+\_\+tree.\+h\char`\"{}}\newline
-Include dependency graph for ivar.\+cpp\+:
-% FIG 0
-\subsection*{Classes}
-\begin{DoxyCompactItemize}
-\item
-struct \mbox{\hyperlink{structargs__t}{args\+\_\+t}}
-\end{DoxyCompactItemize}
-\subsection*{Functions}
-\begin{DoxyCompactItemize}
-\item
-\mbox{\Hypertarget{ivar_8cpp_ae5ad5cbeccaedc03a48d3c7eaa803e79}\label{ivar_8cpp_ae5ad5cbeccaedc03a48d3c7eaa803e79}}
-void {\bfseries print\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_a7d3d88c60168244994ebfb9d01d71aad}\label{ivar_8cpp_a7d3d88c60168244994ebfb9d01d71aad}}
-void {\bfseries print\+\_\+trim\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_a26b660ffee9302a25fc4b85b6fa7f9d9}\label{ivar_8cpp_a26b660ffee9302a25fc4b85b6fa7f9d9}}
-void {\bfseries print\+\_\+variants\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_a494f2b3c1101c4424b73e80d33e4be09}\label{ivar_8cpp_a494f2b3c1101c4424b73e80d33e4be09}}
-void {\bfseries print\+\_\+filtervariants\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_a8499b57df7ba0c00092dd1fd724cd445}\label{ivar_8cpp_a8499b57df7ba0c00092dd1fd724cd445}}
-void {\bfseries print\+\_\+consensus\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_afab6040035caaef89097988ea732ed2c}\label{ivar_8cpp_afab6040035caaef89097988ea732ed2c}}
-void {\bfseries print\+\_\+removereads\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_a27fcc15b0b3c8b4386694af97f09fb91}\label{ivar_8cpp_a27fcc15b0b3c8b4386694af97f09fb91}}
-void {\bfseries print\+\_\+getmasked\+\_\+usage} ()
-\item
-\mbox{\Hypertarget{ivar_8cpp_ac27b7b01a0eb74231c25b3afe477dcae}\label{ivar_8cpp_ac27b7b01a0eb74231c25b3afe477dcae}}
-void {\bfseries print\+\_\+trimadapter\+\_\+usage} ()
-\item
-int \mbox{\hyperlink{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}{main}} (int argc, char $\ast$argv\mbox{[}$\,$\mbox{]})
-\end{DoxyCompactItemize}
-\subsection*{Variables}
-\begin{DoxyCompactItemize}
-\item
-\mbox{\Hypertarget{ivar_8cpp_a1e20c163c03189acfe600030f8ef8b95}\label{ivar_8cpp_a1e20c163c03189acfe600030f8ef8b95}}
-const std\+::string {\bfseries V\+E\+R\+S\+I\+ON} = \char`\"{}1.\+0\char`\"{}
-\item
-\mbox{\Hypertarget{ivar_8cpp_aefc57f4c7b665d04123350d1d1b9fbff}\label{ivar_8cpp_aefc57f4c7b665d04123350d1d1b9fbff}}
-struct \mbox{\hyperlink{structargs__t}{args\+\_\+t}} {\bfseries g\+\_\+args}
-\end{DoxyCompactItemize}
-
-
-\subsection{Function Documentation}
-\mbox{\Hypertarget{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}\label{ivar_8cpp_a0ddf1224851353fc92bfbff6f499fa97}}
-\index{ivar.\+cpp@{ivar.\+cpp}!main@{main}}
-\index{main@{main}!ivar.\+cpp@{ivar.\+cpp}}
-\subsubsection{\texorpdfstring{main()}{main()}}
-{\footnotesize\ttfamily int main (\begin{DoxyParamCaption}\item[{int}]{argc, }\item[{char $\ast$}]{argv\mbox{[}$\,$\mbox{]} }\end{DoxyParamCaption})}
-
-Main Function
-
-This is where the command line arguments into i\+Var are parsed. i\+Var first parses the first argument and depending on the command it either returns the version or uses G\+NU getopt to parse the remaining arguments.
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/9ffe8fb4a6979fa874e5121648b8d338cd2bf63c...1a6ae93ab11c2f26e41a28e970a14a5ef0767d9d
--
View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/9ffe8fb4a6979fa874e5121648b8d338cd2bf63c...1a6ae93ab11c2f26e41a28e970a14a5ef0767d9d
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