Commit 30dedeaf authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.9.26+dfsg

parent b4d2ec55

CMakeLists.txt

+1 −0
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@@ -149,6 +149,7 @@ add_executable(diamond src/run/main.cpp 
  src/tools/tools.cpp

  src/util/system/getRSS.cpp

  src/util/math/sparse_matrix.cpp

  src/lib/tantan/LambdaCalculator.cc

)



if(EXTRA)

README.md

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@@ -21,11 +21,6 @@ Keep posted about new developments by following me on 
![image](https://anaconda.org/bioconda/diamond/badges/platforms.svg)

[![image](https://anaconda.org/bioconda/diamond/badges/downloads.svg)](https://anaconda.org/bioconda/diamond)



Support

=======



The preferred support channel is the [Diamond community website](http://www.diamondsearch.org/). It provides a platform for users to exchange their experiences and get support directly from the developer. You may also use the GitHub issue tracker or send inquiries by email.



Quick start guide

=================
@@ -37,7 +32,7 @@ quick example for setting up and using the program on Linux. 
Installing the software on your system may be done by downloading it in

binary format for immediate use:



    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.25/diamond-linux64.tar.gz

    wget http://github.com/bbuchfink/diamond/releases/download/v0.9.26/diamond-linux64.tar.gz

    tar xzf diamond-linux64.tar.gz



The extracted `diamond` binary file should be moved to a directory
@@ -79,6 +74,11 @@ The output file here is specified with the `–o` option and named 
    BLAST is 10, so by default the program will search a lot more

    stringently than BLAST and not report weak hits.



Support

=======



The preferred support channel is the [Diamond community website](http://www.diamondsearch.org/). It provides a platform for users to exchange their experiences and get support directly from the developer. You may also use the GitHub issue tracker or send inquiries by email.

  

About

=====

build_simple.sh

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@@ -81,4 +81,5 @@ g++ -std=gnu++11 -DNDEBUG -O3 -Wno-deprecated-declarations $1 $2 $3 \ 
  src/tools/tools.cpp \

  src/util/system/getRSS.cpp \

  src/util/math/sparse_matrix.cpp \

  src/lib/tantan/LambdaCalculator.cc \

-lz -lpthread -o diamond

src/ChangeLog

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[0.9.26]

- Fixed a bug that could cause undefined behaviour when using a database file of format version < 2.

- Fixed a compiler error when compiled as generic C++.

- Program will no longer terminate with an error if unlink system call fails.

- Added option `--tantan-minMaskProb` to set minimum repeat probability for tantan masking and changed the default value to 0.9.

- Added option `--tantan-maxRepeatOffset` to set maximum tandem repeat period to consider and changed the default value to 15.

- Added option `--tantan-ungapped` to use tantan in ungapped mode and changed the default to gapped mode.

- Changed score matrix lambda calculation for tantan masking.

- Reference masking is recomputed during alignment runs.



[0.9.25]

- Added support for the `sscinames` output field to print subject scientific names to the tabular output format.

- Fixed a compiler error for GCC 8.2.

src/align/banded_swipe_pipeline.cpp

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@@ -165,7 +165,6 @@ void build_ranking_worker(PtrVector<::Target>::iterator begin, PtrVector<::Targe 


void Pipeline::run(Statistics &stat)

{

	//cout << "Query=" << query_ids::get()[this->query_id].c_str() << endl;

	task_timer timer("Init banded swipe pipeline", target_parallel ? 3 : UINT_MAX);

	Config::set_option(config.padding, 32);

	if (n_targets() == 0)