.travis.yml

+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

-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@debian.org>  Mon, 11 Jun 2018 12:43:20 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Sep 2019 22:55:23 +0200
 
 rampler (1.1.0-1) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -3,10 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@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_;