[med-svn] [spades] 01/04: Imported Upstream version 3.7.1+dfsg
Sascha Steinbiss
sascha at steinbiss.name
Sat Mar 12 07:52:22 UTC 2016
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sascha-guest pushed a commit to branch master
in repository spades.
commit a93a129179b2dc1c3d650c2866d86bd864fac389
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Sat Mar 12 07:23:19 2016 +0000
Imported Upstream version 3.7.1+dfsg
---
VERSION | 2 +-
changelog.html | 14 ++++++----
configs/debruijn/coverage_based_rr.info | 13 ----------
ext/include/city/citycrc.h | 2 +-
ext/src/cityhash/city.cc | 2 +-
manual.html | 38 +++++++++++++--------------
src/cmake/pack.cmake | 4 +--
src/corrector/dataset_processor.cpp | 46 ++++-----------------------------
8 files changed, 38 insertions(+), 83 deletions(-)
diff --git a/VERSION b/VERSION
index 7c69a55..a76ccff 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-3.7.0
+3.7.1
diff --git a/changelog.html b/changelog.html
index 80c05e1..7f16acb 100644
--- a/changelog.html
+++ b/changelog.html
@@ -3,23 +3,27 @@
<h2>SPAdes Genome Assembler changelog</h2>
+<h3>SPAdes 3.7.1, 8 March 2016</h3>
+
+<p>FIX: MismatchCorrector fixed for MaxOS.</p>
+
<h3>SPAdes 3.7.0, 24 February 2016</h3>
-<p>NEW: metaSPAdes metagenomic pipeline.<p>
+<p>NEW: metaSPAdes metagenomic pipeline.</p>
<p>CHANGE: improved performance for both error correction and assembly stages.</p>
-<p>FIX: Multiple bug fixes.<p>
+<p>FIX: Multiple bug fixes.</p>
<h3>SPAdes 3.6.2, 20 November 2015</h3>
-<p>NEW: Contigs/scaffolds paths for assembly_graph.fastg in Bandage-supported format.<p>
+<p>NEW: Contigs/scaffolds paths for assembly_graph.fastg in Bandage-supported format.</p>
<p>FIX: Multithreaded MismatchCorrector.</p>
-<p>FIX: BayesHammer bug fixes.<p>
+<p>FIX: BayesHammer bug fixes.</p>
-<p>FIX: Python 3.5 support; python 3 support for truSPAdes.<p>
+<p>FIX: Python 3.5 support; python 3 support for truSPAdes.</p>
<h3>SPAdes 3.6.1, 4 October 2015</h3>
diff --git a/configs/debruijn/coverage_based_rr.info b/configs/debruijn/coverage_based_rr.info
deleted file mode 100644
index a56dfd1..0000000
--- a/configs/debruijn/coverage_based_rr.info
+++ /dev/null
@@ -1,13 +0,0 @@
-;coverage_based_rr
-
-coverage_based_rr
-{
-coverage_threshold_one_list 0.98
-coverage_threshold_match 0.60
-coverage_threshold_global 5
-tandem_ratio_lower_threshold 0.3
-tandem_ratio_upper_threshold 0.7
-repeat_length_upper_threshold 100
-
-
-}
diff --git a/ext/include/city/citycrc.h b/ext/include/city/citycrc.h
index 318e391..977aeac 100644
--- a/ext/include/city/citycrc.h
+++ b/ext/include/city/citycrc.h
@@ -28,7 +28,7 @@
#ifndef CITY_HASH_CRC_H_
#define CITY_HASH_CRC_H_
-#include <city.h>
+#include <city/city.h>
// Hash function for a byte array.
uint128 CityHashCrc128(const char *s, size_t len);
diff --git a/ext/src/cityhash/city.cc b/ext/src/cityhash/city.cc
index cf9120b..95e5636 100644
--- a/ext/src/cityhash/city.cc
+++ b/ext/src/cityhash/city.cc
@@ -506,7 +506,7 @@ city_uint128 CityHash128(const char *s, size_t len) {
}
#ifdef __SSE4_2__
-#include <citycrc.h>
+#include <city/citycrc.h>
#include <nmmintrin.h>
// Requires len >= 240.
diff --git a/manual.html b/manual.html
index 12f5040..cacb6a9 100644
--- a/manual.html
+++ b/manual.html
@@ -1,6 +1,6 @@
<html>
<head>
- <title>SPAdes 3.7.0 Manual</title>
+ <title>SPAdes 3.7.1 Manual</title>
<style type="text/css">
.code {
background-color: lightgray;
@@ -8,7 +8,7 @@
</style>
</head>
<body>
-<h1>SPAdes 3.7.0 Manual</h1>
+<h1>SPAdes 3.7.1 Manual</h1>
1. <a href="#sec1">About SPAdes</a><br>
1.1. <a href="#sec1.1">Supported data types</a><br>
@@ -35,16 +35,16 @@
<h2>1. About SPAdes</h2>
<p>
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes.
-SPAdes version 3.7.0 was released under GPLv2 on February 24, 2016 and can be downloaded from <a href="http://bioinf.spbau.ru/en/spades" target="_blank">http://bioinf.spbau.ru/en/spades</a>.
+SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from <a href="http://bioinf.spbau.ru/en/spades" target="_blank">http://bioinf.spbau.ru/en/spades</a>.
<a name="sec1.1"></a>
<h3>1.1 Supported data types</h3>
<p>
The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.
<p>
- Version 3.7.0 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.
+ Version 3.7.1 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on single-cell and standard bacterial and fungal data sets. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.
<p>
- SPAdes 3.7.0 also includes metaSPAdes – a pipeline designed specially for metagenomic data sets. To learn more see <a href="#meta">options</a>.
+ SPAdes 3.7.1 also includes metaSPAdes – a pipeline designed specially for metagenomic data sets. To learn more see <a href="#meta">options</a>.
<p>
Additionally, SPAdes has a separate modules for assembling highly polymorphic diploid genomes and for TruSeq barcode assembly. For more information see <a href="dipspades_manual.html" target="_blank">dipSPAdes manual</a> and <a href="truspades_manual.html" target="_blank">truSPAdes manual</a> .
@@ -141,7 +141,7 @@ SPAdes comes in several separate modules:
<li> Running SPAdes without preliminary read error correction (e.g. without BayesHammer or IonHammer) will likely require more time and memory. </li>
<li> Each module removes its temporary files as soon as it finishes. </li>
<li> SPAdes uses 512 Mb per thread for buffers, which results in higher memory consumption. If you set memory limit manually, SPAdes will use smaller buffers and thus less RAM. </li>
- <li> Performance statistics is given for SPAdes version 3.7.0. </li>
+ <li> Performance statistics is given for SPAdes version 3.7.1. </li>
</ul>
@@ -155,13 +155,13 @@ SPAdes comes in several separate modules:
<h3>2.1 Downloading SPAdes Linux binaries</h3>
<p>
- To download <a href="http://spades.bioinf.spbau.ru/release3.7.0/SPAdes-3.7.0-Linux.tar.gz">SPAdes Linux binaries</a> and extract them, go to the directory in which you wish SPAdes to be installed and run:
+ To download <a href="http://spades.bioinf.spbau.ru/release3.7.1/SPAdes-3.7.1-Linux.tar.gz">SPAdes Linux binaries</a> and extract them, go to the directory in which you wish SPAdes to be installed and run:
<pre class="code">
<code>
- wget http://spades.bioinf.spbau.ru/release3.7.0/SPAdes-3.7.0-Linux.tar.gz
- tar -xzf SPAdes-3.7.0-Linux.tar.gz
- cd SPAdes-3.7.0-Linux/bin/
+ wget http://spades.bioinf.spbau.ru/release3.7.1/SPAdes-3.7.1-Linux.tar.gz
+ tar -xzf SPAdes-3.7.1-Linux.tar.gz
+ cd SPAdes-3.7.1-Linux/bin/
</code>
</pre>
@@ -187,13 +187,13 @@ SPAdes comes in several separate modules:
<h3>2.2 Downloading SPAdes binaries for Mac</h3>
<p>
- To obtain <a href="http://spades.bioinf.spbau.ru/release3.7.0/SPAdes-3.7.0-Darwin.tar.gz">SPAdes binaries for Mac</a>, go to the directory in which you wish SPAdes to be installed and run:
+ To obtain <a href="http://spades.bioinf.spbau.ru/release3.7.1/SPAdes-3.7.1-Darwin.tar.gz">SPAdes binaries for Mac</a>, go to the directory in which you wish SPAdes to be installed and run:
<pre class="code">
<code>
- curl http://spades.bioinf.spbau.ru/release3.7.0/SPAdes-3.7.0-Darwin.tar.gz -o SPAdes-3.7.0-Darwin.tar.gz
- tar -zxf SPAdes-3.7.0-Darwin.tar.gz
- cd SPAdes-3.7.0-Darwin/bin/
+ curl http://spades.bioinf.spbau.ru/release3.7.1/SPAdes-3.7.1-Darwin.tar.gz -o SPAdes-3.7.1-Darwin.tar.gz
+ tar -zxf SPAdes-3.7.1-Darwin.tar.gz
+ cd SPAdes-3.7.1-Darwin/bin/
</code>
</pre>
@@ -228,13 +228,13 @@ SPAdes comes in several separate modules:
</ul>
<p>
- If you meet these requirements, you can download the <a href="http://spades.bioinf.spbau.ru/release3.7.0/SPAdes-3.7.0.tar.gz">SPAdes source code</a>:
+ If you meet these requirements, you can download the <a href="http://spades.bioinf.spbau.ru/release3.7.1/SPAdes-3.7.1.tar.gz">SPAdes source code</a>:
<pre class="code">
<code>
- wget http://spades.bioinf.spbau.ru/release3.7.0/SPAdes-3.7.0.tar.gz
- tar -xzf SPAdes-3.7.0.tar.gz
- cd SPAdes-3.7.0
+ wget http://spades.bioinf.spbau.ru/release3.7.1/SPAdes-3.7.1.tar.gz
+ tar -xzf SPAdes-3.7.1.tar.gz
+ cd SPAdes-3.7.1
</code>
</pre>
@@ -338,7 +338,7 @@ Thank you for using SPAdes!
SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.
<p>
- To run SPAdes 3.7.0 you need at least one library of the following types:
+ To run SPAdes 3.7.1 you need at least one library of the following types:
<ul>
<li>Illumina paired-end/high-quality mate-pairs/unpaired reads</li>
<li>IonTorrent paired-end/high-quality mate-pairs/unpaired reads</li>
diff --git a/src/cmake/pack.cmake b/src/cmake/pack.cmake
index 73bf02f..089b9f2 100644
--- a/src/cmake/pack.cmake
+++ b/src/cmake/pack.cmake
@@ -12,10 +12,10 @@ set(CPACK_PACKAGE_NAME "SPAdes")
set(CPACK_PACKAGE_VENDOR "Saint Petersburg Academic University")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${SPADES_MAIN_SRC_DIR}/../README")
set(CPACK_RESOURCE_FILE_LICENSE "${SPADES_MAIN_SRC_DIR}/../LICENSE")
-set(CPACK_PACKAGE_VERSION "3.7.0")
+set(CPACK_PACKAGE_VERSION "3.7.1")
set(CPACK_PACKAGE_VERSION_MAJOR "3")
set(CPACK_PACKAGE_VERSION_MINOR "7")
-set(CPACK_PACKAGE_VERSION_PATCH "0")
+set(CPACK_PACKAGE_VERSION_PATCH "1")
set(CPACK_STRIP_FILES bin/spades bin/hammer bin/ionhammer bin/dipspades bin/spades-bwa bin/corrector bin/scaffold_correction)
# Source stuff
diff --git a/src/corrector/dataset_processor.cpp b/src/corrector/dataset_processor.cpp
index 94dd8f6..8cb2d38 100644
--- a/src/corrector/dataset_processor.cpp
+++ b/src/corrector/dataset_processor.cpp
@@ -139,7 +139,7 @@ string DatasetProcessor::RunPairedBwa(const string &left, const string &right, c
string isize_txt_filename = path::append_path(cur_dir, "isize.txt");
string tmp_file = path::append_path(cur_dir, "bwa.flood");
- string index_line = corr_cfg::get().bwa + string(" index ") + "-a " + "is " + genome_file_ + " " + " 2>" + tmp_file;
+ string index_line = corr_cfg::get().bwa + string(" index ") + "-a " + "is " + genome_file_ ;
INFO("Running bwa index ...: " << index_line);
run_res = system(index_line.c_str());
if (run_res != 0) {
@@ -147,34 +147,14 @@ string DatasetProcessor::RunPairedBwa(const string &left, const string &right, c
return "";
}
string nthreads_str = to_string(nthreads_);
-/* string left_line = corr_cfg::get().bwa + " aln " + genome_file_ + " " + left + " -t " + nthreads_str + " -O 7 -E 2 -k 3 -n 0.08 -q 15 > "
- + tmp1_sai_filename + " 2>" + tmp_file;
-
- string right_line = corr_cfg::get().bwa + " aln " + genome_file_ + " " + right + " -t " + nthreads_str + " -O 7 -E 2 -k 3 -n 0.08 -q 15 > "
- + tmp2_sai_filename + " 2>" + tmp_file;
- INFO("Running bwa aln ...: " << left_line);
- int res1 = system(left_line.c_str());
- INFO("Running bwa aln ...: " << right_line);
- int res2 = system(right_line.c_str());
- if (res1 != 0 || res2 != 0) {
- INFO("bwa failed, skipping sublib");
- return "";
- }
-*/
- string last_line = corr_cfg::get().bwa + string(" mem ") + genome_file_ + " " + left + " " + right + " -t " + nthreads_str + " > "
- + tmp_sam_filename + " 2>" + isize_txt_filename;
+ string last_line = corr_cfg::get().bwa + string(" mem ") + " -v 1 -t " + nthreads_str + " "+ genome_file_ + " " + left + " " + right + " > "
+ + tmp_sam_filename ;
INFO("Running bwa mem ...:" << last_line);
run_res = system(last_line.c_str());
if (run_res != 0) {
INFO("bwa failed, skipping sublib");
return "";
}
-/* res1 = unlink(tmp1_sai_filename.c_str());
- res2 = unlink(tmp2_sai_filename.c_str());
- if (res1 != 0 || res2 != 0) {
- INFO("Failed to delete temporary sai files");
- }
-*/
return tmp_sam_filename;
}
@@ -186,7 +166,7 @@ string DatasetProcessor::RunSingleBwa(const string &single, const size_t lib) {
string isize_txt_filename = path::append_path(cur_dir, "isize.txt");
string tmp_file = path::append_path(cur_dir, "bwa.flood");
- string index_line = corr_cfg::get().bwa + string(" index ") + "-a " + "is " + genome_file_ + " 2 " + "2>" + tmp_file;
+ string index_line = corr_cfg::get().bwa + string(" index ") + "-a " + "is " + genome_file_ ;
INFO("Running bwa index ...: " << index_line);
run_res = system(index_line.c_str());
if (run_res != 0) {
@@ -194,29 +174,13 @@ string DatasetProcessor::RunSingleBwa(const string &single, const size_t lib) {
return "";
}
string nthreads_str = to_string(nthreads_);
-/* string single_sai_line = corr_cfg::get().bwa + " aln " + genome_file_ + " " + single + " -t " + nthreads_str + " -O 7 -E 2 -k 3 -n 0.08 -q 15 > "
- + tmp_sai_filename + " 2>" + tmp_file;
-
- INFO("Running bwa aln ...:" + single_sai_line);
-
- run_res = system(single_sai_line.c_str());
- if (run_res != 0) {
- INFO("bwa failed, skipping sublib");
- return "";
- }*/
- string last_line = corr_cfg::get().bwa + " mem " + genome_file_ + " " + single + " -t " + nthreads_str + " > " + tmp_sam_filename + " 2>"
- + isize_txt_filename;
+ string last_line = corr_cfg::get().bwa + " mem "+ " -v 1 -t " + nthreads_str + " " + genome_file_ + " " + single + " > " + tmp_sam_filename;
INFO("Running bwa mem ...:" << last_line);
run_res = system(last_line.c_str());
if (run_res != 0) {
INFO("bwa failed, skipping sublib");
return "";
}
-/* run_res = unlink(tmp_sai_filename.c_str());
- if (run_res != 0) {
- INFO("Failed to delete temporary sai files");
- }
-*/
return tmp_sam_filename;
}
--
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