[med-svn] [Git][med-team/rampler][upstream] New upstream version 1.1.1

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / rampler


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


4 changed files:

- .travis.yml
- README.md
- 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+


=====================================
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/commit/6c018464f6e9f6cb308425878e02598f77b8f38d

-- 
View it on GitLab: https://salsa.debian.org/med-team/rampler/commit/6c018464f6e9f6cb308425878e02598f77b8f38d
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190905/64a4475d/attachment-0001.html>