[med-svn] [Git][med-team/rampler][master] 7 commits: New upstream version 1.1.1

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / rampler


Commits:
6c018464 by Andreas Tille at 2019-09-05T20:52:34Z
New upstream version 1.1.1
- - - - -
8866fe59 by Andreas Tille at 2019-09-05T20:52:34Z
New upstream version

- - - - -
959a080e by Andreas Tille at 2019-09-05T20:52:34Z
Update upstream source from tag 'upstream/1.1.1'

Update to upstream version '1.1.1'
with Debian dir 2b12aa9d3cb92446a4eff1e43e9102906e32a5d8
- - - - -
46659586 by Andreas Tille at 2019-09-05T20:52:34Z
debhelper-compat 12

- - - - -
e62780d6 by Andreas Tille at 2019-09-05T20:52:36Z
Standards-Version: 4.4.0

- - - - -
cf2194cf by Andreas Tille at 2019-09-05T20:55:14Z
Close bug

- - - - -
699a30bc by Andreas Tille at 2019-09-05T20:55:53Z
Upload to unstable

- - - - -


7 changed files:

- .travis.yml
- README.md
- debian/changelog
- − debian/compat
- debian/control
- src/main.cpp
- src/sampler.cpp


Changes:

=====================================
.travis.yml
=====================================
@@ -1,3 +1,5 @@
+dist: trusty
+
 language: cpp
 
 compiler:


=====================================
README.md
=====================================
@@ -3,7 +3,9 @@
 [![Latest GitHub release](https://img.shields.io/github/release/rvaser/rampler.svg)](https://github.com/rvaser/rampler/releases/latest)
 [![Build status for c++/clang++](https://travis-ci.org/rvaser/rampler.svg?branch=master)](https://travis-ci.org/rvaser/rampler)
 
-Module for sampling genomic sequences.
+Standalone module for sampling genomic sequences. It supports two modes, random subsampling of sequencer data to a desired depth (given the reference length) and file splitting to desired size in bytes.
+
+Rampler takes as first input argument a file in FASTA/FASTQ format which can be compressed with gzip. The rest of input parameters depend on the mode of operation. The output is stored into a file(s) which is in the same format as the input file but uncompressed.
 
 ## Dependencies
 1. gcc 4.8+ or clang 3.4+


=====================================
debian/changelog
=====================================
@@ -1,8 +1,12 @@
-rampler (1.1.0-2) UNRELEASED; urgency=medium
+rampler (1.1.1-1) unstable; urgency=medium
 
+  * New upstream version
+    Closes: #935293
   * Enhanced description
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
 
- -- Andreas Tille <tille at debian.org>  Mon, 11 Jun 2018 12:43:20 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 05 Sep 2019 22:55:23 +0200
 
 rampler (1.1.0-1) unstable; urgency=medium
 


=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -3,10 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                cmake,
                libbioparser-dev
-Standards-Version: 4.1.4
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/rampler
 Vcs-Git: https://salsa.debian.org/med-team/rampler.git
 Homepage: https://github.com/rvaser/rampler


=====================================
src/main.cpp
=====================================
@@ -7,7 +7,7 @@
 
 #include "bioparser/bioparser.hpp"
 
-static const char* version = "v1.1.0";
+static const char* version = "v1.1.1";
 
 static struct option options[] = {
     {"out-directory", required_argument, 0, 'o'},


=====================================
src/sampler.cpp
=====================================
@@ -72,7 +72,7 @@ void Sampler::initialize() {
     sparser_->reset();
     while (true) {
         std::vector<std::unique_ptr<Sequence>> sequences;
-        auto status = sparser_->parse_objects(sequences, kChunkSize);
+        auto status = sparser_->parse(sequences, kChunkSize);
 
         for (const auto& it: sequences) {
             sequences_length_ += it->data().size();
@@ -112,7 +112,7 @@ void Sampler::subsample(const std::string& out_directory, uint32_t reference_len
     sparser_->reset();
     while (true) {
         std::vector<std::unique_ptr<Sequence>> sequences;
-        auto status = sparser_->parse_objects(sequences, kChunkSize);
+        auto status = sparser_->parse(sequences, kChunkSize);
 
         for (const auto& it: sequences) {
             if (distribution(generator) < ratio) {
@@ -147,7 +147,7 @@ void Sampler::split(const std::string& out_directory, uint32_t chunk_size) {
     sparser_->reset();
     while (true) {
         std::vector<std::unique_ptr<Sequence>> sequences;
-        auto status = sparser_->parse_objects(sequences, chunk_size);
+        auto status = sparser_->parse(sequences, chunk_size);
 
         std::string out_path = out_directory + "/" + base_name_ + "_" +
             std::to_string(chunk_number) + extension_;



View it on GitLab: https://salsa.debian.org/med-team/rampler/compare/20b758cb0d74b2ac00c14bb67f889fb8b38374f2...699a30bc7419debe808c6cc2b1995998a0b49ab1

-- 
View it on GitLab: https://salsa.debian.org/med-team/rampler/compare/20b758cb0d74b2ac00c14bb67f889fb8b38374f2...699a30bc7419debe808c6cc2b1995998a0b49ab1
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