[med-svn] [Git][med-team/bowtie2][upstream] New upstream version 2.5.4
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Aug 7 12:42:26 BST 2024
Andreas Tille pushed to branch upstream at Debian Med / bowtie2
Commits:
5d6c8de7 by Andreas Tille at 2024-08-07T11:50:16+02:00
New upstream version 2.5.4
- - - - -
19 changed files:
- .github/workflows/random-tests.yml
- .github/workflows/simple-tests.yml
- BOWTIE2_VERSION
- MANUAL
- MANUAL.markdown
- NEWS
- README.md
- aln_sink.cpp
- bt2_idx.h
- bt2_search.cpp
- doc/manual.html
- doc/website/manual.ssi
- doc/website/recent_news.ssi
- doc/website/rhsidebar.ssi
- filebuf.h
- opts.h
- pat.cpp
- sam.h
- tokenize.h
Changes:
=====================================
.github/workflows/random-tests.yml
=====================================
@@ -60,6 +60,10 @@ jobs:
runs-on: macos-latest
steps:
- uses: actions/checkout at v2
+ - name: Pull submodules
+ run: |
+ git submodule init
+ git submodule update
- name: Run random tests
run: |
make clean; make -j4 allall
=====================================
.github/workflows/simple-tests.yml
=====================================
@@ -58,6 +58,10 @@ jobs:
runs-on: macos-latest
steps:
- uses: actions/checkout at v2
+ - name: Pull submodules
+ run: |
+ git submodule init
+ git submodule update
- name: Run simple tests
run: |
make clean; make -j4 allall
=====================================
BOWTIE2_VERSION
=====================================
@@ -1 +1 @@
-2.5.3
+2.5.4
=====================================
MANUAL
=====================================
@@ -153,28 +153,33 @@ wrapper will help determine the appropriate index type for uncompressed
and gzipped inputs.
To build bowtie2-build with libsais first make sure that the libsais
-submodule is available. This can be done in one of the following ways: *
-first time cloning bowtie2 --
-git clone --recursive https://github.com/BenLangmead/bowtie2.git *
-existing checkout of bowtie2 --
-git submodule init && git submodule update
+submodule is available. This can be done in one of the following ways:
-Issue the following command line to build libsais: * with OpenMP support
--- [g]make libsais USE_SAIS_OPENMP=1 * without OpenMP support --
-[g]make libsais USE_SAIS=1
+- first time cloning bowtie2 --
+ git clone --recursive https://github.com/BenLangmead/bowtie2.git
+- existing checkout of bowtie2 --
+ git submodule init && git submodule update
+
+Issue the following command line to build libsais:
+
+- with OpenMP support -- [g]make libsais USE_SAIS_OPENMP=1
+- without OpenMP support -- [g]make libsais USE_SAIS=1
The choice of using OpenMP will determine whether or not the algorithm
runs multithreaded. The [-p/--threads] argument to bowtie2-build will be
ignored when libsais is compiled without OpenMP support.
-Finally, building the build executable: * with OpenMP support --
-[g]make bowtie2-build-s USE_SAIS_OPENMP=1 * without OpenMP support --
-[g]make bowtie2-build-s USE_SAIS=1
+Finally, building the bowtie2-build executable:
+
+- with OpenMP support -- [g]make bowtie2-build-s USE_SAIS_OPENMP=1
+- without OpenMP support -- [g]make bowtie2-build-s USE_SAIS=1
Building with CMake
To build Bowtie2 with SRA and libsais support issue the following
-command: * cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .
+command:
+
+- cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .
CMake will take care of building and linking against the specified
dependencies.
@@ -816,7 +821,7 @@ alignment to be considered valid, and x is the read length.
Usage
- bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]
+ bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | -b <bam>} -S [<sam>]
Main arguments
@@ -1489,6 +1494,17 @@ Use '='/'X', instead of 'M', to specify matches/mismatches in SAM record
Append FASTA/FASTQ comment to SAM record, where a comment is everything
after the first space in the read name.
+ --sam-opt-config <config>
+
+Use <config> to toggle SAM Optional Fields where <config> is a string of
+comma delimited, case-insensitive, two-letter tags. Tags prefixed with a
+"-" will be turned off and hence will not be included in the SAM output.
+The example below turns off the "MD" tag and enables the
+bowtie2-specific "YP" tag. The config is additive, so, any default OPT
+flags that need to be turned off will have to explicitly specified.
+
+ `bowtie2 ... --sam-opt-config "-md,yp"
+
Performance options
-o/--offrate <int>
=====================================
MANUAL.markdown
=====================================
@@ -158,10 +158,12 @@ will help determine the appropriate index type for uncompressed and gzipped inpu
To build `bowtie2-build` with [libsais] first make sure that the libsais submodule
is available. This can be done in one of the following ways:
+
* first time cloning bowtie2 -- `git clone --recursive https://github.com/BenLangmead/bowtie2.git`
* existing checkout of bowtie2 -- `git submodule init && git submodule update`
Issue the following command line to build libsais:
+
* with OpenMP support -- `[g]make libsais USE_SAIS_OPENMP=1`
* without OpenMP support -- `[g]make libsais USE_SAIS=1`
@@ -169,13 +171,15 @@ The choice of using OpenMP will determine whether or not the algorithm
runs multithreaded. The [`-p/--threads`] argument to `bowtie2-build` will
be ignored when libsais is compiled without OpenMP support.
-Finally, building the build executable:
+Finally, building the bowtie2-build executable:
+
* with OpenMP support -- `[g]make bowtie2-build-s USE_SAIS_OPENMP=1`
* without OpenMP support -- `[g]make bowtie2-build-s USE_SAIS=1`
### Building with CMake ###
To build Bowtie2 with SRA and libsais support issue the following command:
+
* `cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .`
CMake will take care of building and linking against the specified dependencies.
@@ -813,7 +817,7 @@ considered valid, and `x` is the read length.
### Usage
- bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]
+ bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | -b <bam>} -S [<sam>]
### Main arguments
@@ -1908,6 +1912,23 @@ Use `'='/'X'`, instead of `'M'`, to specify matches/mismatches in SAM record
Append FASTA/FASTQ comment to SAM record, where a comment is everything
after the first space in the read name.
+</td></tr>
+<tr><td id="bowtie2-options-sam-opt-config">
+
+ --sam-opt-config <config>
+
+</td><td>
+
+Use `<config>` to toggle SAM Optional Fields where `<config>` is a
+string of comma delimited, case-insensitive, two-letter tags. Tags
+prefixed with a "-" will be turned off and hence will not be included
+in the SAM output. The example below turns off the "MD" tag and
+enables the `bowtie2`-specific "YP" tag. The config is additive, so,
+any default OPT flags that need to be turned off will have to
+explicitly specified.
+
+ `bowtie2 ... --sam-opt-config "-md,yp"
+
</td></tr>
</table>
@@ -2931,6 +2952,8 @@ for more details and variations on this process.
[`--very-sensitive-local`]: #bowtie2-options-very-sensitive-local
[`--very-sensitive`]: #bowtie2-options-very-sensitive
[`--xeq`]: #bowtie2-options-xeq
+[`--sam-append-comment`]: #bowtie2-options-sam-append-comment
+[`--sam-opt-config`]: #bowtie2-options-sam-opt-config
[`-1`]: #bowtie2-options-1
[`-2`]: #bowtie2-options-2
[`-3`/`--trim3`]: #bowtie2-options-3
=====================================
NEWS
=====================================
@@ -4,7 +4,7 @@ Bowtie 2 NEWS
Bowtie 2 is available for download from the project website,
http://bowtie-bio.sf.net/bowtie2 and on Github,
https://github.com/BenLangmead/bowtie2/releases. 2.0.0-beta1 is
-the first version released to the public and 2.5.3 is the latest
+the first version released to the public and 2.5.4 is the latest
version. Bowtie 2 is licensed under the GPLv3 license. See `LICENSE'
file for details.
@@ -19,6 +19,20 @@ Please report any issues to the Bowtie 2 Github page or using the Sourceforge bu
Version Release History
=======================
+## Version 2.5.4 - May 16, 2024 ##
+
+### bowtie2 ###
+ * Added `--sam-opt-config` command line option for toggling SAM Opt flags.
+ See MANUAL for details.
+ * Fixed an issue causing `bowtie2`'s memory usage to increase over time
+ when aligning BAM files.
+ * Changed bowtie2 to continue flushing output in the event of a partial write.
+ * Changed the behavior of `bowtie2-build` to throw an exception if it is unable
+ to write the BWT (.1.bt2, .1.rev.bt2). In prior versions `bowtie2-build`, would silently
+ ignore the error which has led some to report the absence of the BWT files in
+ a "completed" index build.
+ * Reverted the changes made in v2.5.0 that sometimes caused unique concordant alignments to be overcounted.
+
## Version 2.5.3 - Jan 16, 2024 ##
* Fixed an issue causing `bowtie2`'s memory usage to increase over time.
=====================================
README.md
=====================================
@@ -2,7 +2,7 @@
<!-- badges: start -->
-[](https://shields.io/)
+[](https://shields.io/)
<!-- [](https://travis-ci.org/BenLangmead/bowtie2) -->
[](https://www.gnu.org/licenses/gpl-3.0)
<!--badges: end -->
=====================================
aln_sink.cpp
=====================================
@@ -834,9 +834,8 @@ void AlnSinkWrap::finishRead(
} else {
met.nconcord_uni++;
assert(!rs1_.empty());
- AlnScore sc1 = concordSumm.bestUnchosenP1Score();
- AlnScore sc2 = concordSumm.bestUnchosenP2Score();
- if(!sc1.valid() && !sc2.valid()) {
+
+ if(!concordSumm.bestUnchosenCScore().valid()) {
met.nconcord_uni1++;
} else {
met.nconcord_uni2++;
=====================================
bt2_idx.h
=====================================
@@ -672,14 +672,17 @@ public:
_in2Str = file + ".2." + gEbwt_ext + ".tmp";
packed_ = packed;
// Open output files
- ofstream fout1(_in1Str.c_str(), ios::binary);
+ ofstream fout1(_in1Str.c_str(), ios::binary);
+ fout1.exceptions(ofstream::failbit | ofstream::badbit | ofstream::eofbit);
if(!fout1.good()) {
cerr << "Could not open index file for writing: \"" << _in1Str.c_str() << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
<< "Bowtie." << endl;
throw 1;
- }
- ofstream fout2(_in2Str.c_str(), ios::binary);
+ }
+
+ ofstream fout2(_in2Str.c_str(), ios::binary);
+ fout2.exceptions(ofstream::failbit | ofstream::badbit | ofstream::eofbit);
if(!fout2.good()) {
cerr << "Could not open index file for writing: \"" << _in2Str.c_str() << "\"" << endl
<< "Please make sure the directory exists and that permissions allow writing by" << endl
=====================================
bt2_search.cpp
=====================================
@@ -171,6 +171,7 @@ static bool sam_print_zi;
static bool sam_print_zp;
static bool sam_print_zu;
static bool sam_print_zt;
+static EList<string> sam_opt_flags;
static bool preserve_tags; // Only applies when aligning BAM files
static bool align_paired_reads; // Process only the paired reads in BAM file
static bool bwaSwLike;
@@ -670,6 +671,7 @@ static struct option long_options[] = {
{(char*)"sra-acc", required_argument, 0, ARG_SRA_ACC},
#endif
{(char*)"sam-append-comment", no_argument, 0, ARG_SAM_APPEND_COMMENT},
+ {(char*)"sam-opt-config", required_argument, 0, ARG_SAM_OPT_CONFIG},
{(char*)0, 0, 0, 0} // terminator
};
@@ -876,9 +878,11 @@ static void printUsage(ostream& out) {
<< " at the expense of generating non-standard SAM." << endl
<< " --xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record." << endl
<< " --soft-clipped-unmapped-tlen" << endl
- << " Exclude soft-clipped bases when reporting TLEN" << endl
+ << " Exclude soft-clipped bases when reporting TLEN." << endl
<< " --sam-append-comment" << endl
- << " Append FASTA/FASTQ comment to SAM record" << endl
+ << " Append FASTA/FASTQ comment to SAM record." << endl
+ << " --sam-opt-config <config>" << endl
+ << " Use <config>, example '-MD,YP,-AS', to toggle SAM Optional fields." << endl
<< endl
<< " Performance:" << endl
// << " -o/--offrate <int> override offrate of index; must be >= index's offrate" << endl
@@ -1555,6 +1559,16 @@ static void parseOption(int next_option, const char *arg) {
}
break;
}
+ case ARG_SAM_OPT_CONFIG: {
+ // string no_defaults("-as,-xs,-xn,-x0,-x1,-xm,-xo,-xg,-nm,-md,-yf,-yt,-ys");
+ // string defaults("as,xs,xn,x0,x1,xm,xo,xg,nm,md,yf,yt,ys");
+
+ // if (strncmp(arg, "-default", 8) == 0) {
+ // no_defaults += arg;
+ // }
+ tokenize(arg, ",", sam_opt_flags);
+ break;
+ }
case ARG_DESC: printArgDesc(cout); throw 0;
case 'S': outfile = arg; break;
case 'U': {
@@ -4990,6 +5004,12 @@ static void driver(
sam_print_zp,
sam_print_zu,
sam_print_zt);
+
+ if (sam_opt_flags.size() > 0) {
+ for (size_t i = 0; i < sam_opt_flags.size(); i++) {
+ samc.toggleOptFlagByName(sam_opt_flags[i]);
+ }
+ }
// Set up hit sink; if sanityCheck && !os.empty() is true,
// then instruct the sink to "retain" hits in a vector in
// memory so that we can easily sanity check them later on
=====================================
doc/manual.html
=====================================
@@ -23,9 +23,6 @@
.display.math{display: block; text-align: center; margin: 0.5rem auto;}
</style>
<link rel="stylesheet" href="doc/style.css" />
- <!--[if lt IE 9]>
- <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
- <![endif]-->
</head>
<body>
<h1>Table of Contents</h1>
@@ -372,24 +369,37 @@ index type for uncompressed and gzipped inputs.</p>
<p>To build <code>bowtie2-build</code> with <a
href="https://github.com/IlyaGrebnov/libsais">libsais</a> first make
sure that the libsais submodule is available. This can be done in one of
-the following ways: * first time cloning bowtie2 --
-<code>git clone --recursive https://github.com/BenLangmead/bowtie2.git</code>
-* existing checkout of bowtie2 --
-<code>git submodule init && git submodule update</code></p>
-<p>Issue the following command line to build libsais: * with OpenMP
-support -- <code>[g]make libsais USE_SAIS_OPENMP=1</code> * without
-OpenMP support -- <code>[g]make libsais USE_SAIS=1</code></p>
+the following ways:</p>
+<ul>
+<li>first time cloning bowtie2 --
+<code>git clone --recursive https://github.com/BenLangmead/bowtie2.git</code></li>
+<li>existing checkout of bowtie2 --
+<code>git submodule init && git submodule update</code></li>
+</ul>
+<p>Issue the following command line to build libsais:</p>
+<ul>
+<li>with OpenMP support --
+<code>[g]make libsais USE_SAIS_OPENMP=1</code></li>
+<li>without OpenMP support --
+<code>[g]make libsais USE_SAIS=1</code></li>
+</ul>
<p>The choice of using OpenMP will determine whether or not the
algorithm runs multithreaded. The [<code>-p/--threads</code>] argument
to <code>bowtie2-build</code> will be ignored when libsais is compiled
without OpenMP support.</p>
-<p>Finally, building the build executable: * with OpenMP support --
-<code>[g]make bowtie2-build-s USE_SAIS_OPENMP=1</code> * without OpenMP
-support -- <code>[g]make bowtie2-build-s USE_SAIS=1</code></p>
+<p>Finally, building the bowtie2-build executable:</p>
+<ul>
+<li>with OpenMP support --
+<code>[g]make bowtie2-build-s USE_SAIS_OPENMP=1</code></li>
+<li>without OpenMP support --
+<code>[g]make bowtie2-build-s USE_SAIS=1</code></li>
+</ul>
<h3 id="building-with-cmake">Building with CMake</h3>
<p>To build Bowtie2 with SRA and libsais support issue the following
-command: *
-<code>cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .</code></p>
+command:</p>
+<ul>
+<li><code>cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .</code></li>
+</ul>
<p>CMake will take care of building and linking against the specified
dependencies.</p>
<h2 id="adding-to-path">Adding to PATH</h2>
@@ -1027,7 +1037,7 @@ the function <code>f(x)</code> sets the minimum alignment score
necessary for an alignment to be considered valid, and <code>x</code> is
the read length.</p>
<h3 id="usage">Usage</h3>
-<pre><code>bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]</code></pre>
+<pre><code>bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | -b <bam>} -S [<sam>]</code></pre>
<h3 id="main-arguments">Main arguments</h3>
<table>
<tr>
@@ -2183,6 +2193,22 @@ matches/mismatches in SAM record</p>
everything after the first space in the read name.</p>
</td>
</tr>
+<tr>
+<td id="bowtie2-options-sam-opt-config">
+<pre><code>--sam-opt-config <config></code></pre>
+</td>
+<td>
+<p>Use <code><config></code> to toggle SAM Optional Fields where
+<code><config></code> is a string of comma delimited,
+case-insensitive, two-letter tags. Tags prefixed with a "-" will be
+turned off and hence will not be included in the SAM output. The example
+below turns off the "MD" tag and enables the
+<code>bowtie2</code>-specific "YP" tag. The config is additive, so, any
+default OPT flags that need to be turned off will have to explicitly
+specified.</p>
+<pre><code>`bowtie2 ... --sam-opt-config "-md,yp"</code></pre>
+</td>
+</tr>
</table>
<h4 id="performance-options">Performance options</h4>
<table>
=====================================
doc/website/manual.ssi
=====================================
@@ -338,24 +338,37 @@ index type for uncompressed and gzipped inputs.</p>
<p>To build <code>bowtie2-build</code> with <a
href="https://github.com/IlyaGrebnov/libsais">libsais</a> first make
sure that the libsais submodule is available. This can be done in one of
-the following ways: * first time cloning bowtie2 --
-<code>git clone --recursive https://github.com/BenLangmead/bowtie2.git</code>
-* existing checkout of bowtie2 --
-<code>git submodule init && git submodule update</code></p>
-<p>Issue the following command line to build libsais: * with OpenMP
-support -- <code>[g]make libsais USE_SAIS_OPENMP=1</code> * without
-OpenMP support -- <code>[g]make libsais USE_SAIS=1</code></p>
+the following ways:</p>
+<ul>
+<li>first time cloning bowtie2 --
+<code>git clone --recursive https://github.com/BenLangmead/bowtie2.git</code></li>
+<li>existing checkout of bowtie2 --
+<code>git submodule init && git submodule update</code></li>
+</ul>
+<p>Issue the following command line to build libsais:</p>
+<ul>
+<li>with OpenMP support --
+<code>[g]make libsais USE_SAIS_OPENMP=1</code></li>
+<li>without OpenMP support --
+<code>[g]make libsais USE_SAIS=1</code></li>
+</ul>
<p>The choice of using OpenMP will determine whether or not the
algorithm runs multithreaded. The [<code>-p/--threads</code>] argument
to <code>bowtie2-build</code> will be ignored when libsais is compiled
without OpenMP support.</p>
-<p>Finally, building the build executable: * with OpenMP support --
-<code>[g]make bowtie2-build-s USE_SAIS_OPENMP=1</code> * without OpenMP
-support -- <code>[g]make bowtie2-build-s USE_SAIS=1</code></p>
+<p>Finally, building the bowtie2-build executable:</p>
+<ul>
+<li>with OpenMP support --
+<code>[g]make bowtie2-build-s USE_SAIS_OPENMP=1</code></li>
+<li>without OpenMP support --
+<code>[g]make bowtie2-build-s USE_SAIS=1</code></li>
+</ul>
<h3 id="building-with-cmake">Building with CMake</h3>
<p>To build Bowtie2 with SRA and libsais support issue the following
-command: *
-<code>cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .</code></p>
+command:</p>
+<ul>
+<li><code>cmake . -D USE_SRA=1 -D USE_SAIS=1 && cmake --build .</code></li>
+</ul>
<p>CMake will take care of building and linking against the specified
dependencies.</p>
<h2 id="adding-to-path">Adding to PATH</h2>
@@ -993,7 +1006,7 @@ the function <code>f(x)</code> sets the minimum alignment score
necessary for an alignment to be considered valid, and <code>x</code> is
the read length.</p>
<h3 id="usage">Usage</h3>
-<pre><code>bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | b <bam>} -S [<sam>]</code></pre>
+<pre><code>bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | --sra-acc <acc> | -b <bam>} -S [<sam>]</code></pre>
<h3 id="main-arguments">Main arguments</h3>
<table>
<tr>
@@ -2149,6 +2162,22 @@ matches/mismatches in SAM record</p>
everything after the first space in the read name.</p>
</td>
</tr>
+<tr>
+<td id="bowtie2-options-sam-opt-config">
+<pre><code>--sam-opt-config <config></code></pre>
+</td>
+<td>
+<p>Use <code><config></code> to toggle SAM Optional Fields where
+<code><config></code> is a string of comma delimited,
+case-insensitive, two-letter tags. Tags prefixed with a "-" will be
+turned off and hence will not be included in the SAM output. The example
+below turns off the "MD" tag and enables the
+<code>bowtie2</code>-specific "YP" tag. The config is additive, so, any
+default OPT flags that need to be turned off will have to explicitly
+specified.</p>
+<pre><code>`bowtie2 ... --sam-opt-config "-md,yp"</code></pre>
+</td>
+</tr>
</table>
<h4 id="performance-options">Performance options</h4>
<table>
=====================================
doc/website/recent_news.ssi
=====================================
@@ -1,3 +1,28 @@
+<h2 id="version-2.5.4---may-16-2024">Version 2.5.4 - May 16, 2024</h2>
+<h3 id="bowtie2">bowtie2</h3>
+<ul>
+ <li>Added <code><a href="manual.shtml#bowtie2-sam-opt-config">--sam-opt-config</a></code> command line option for toggling
+ SAM Opt flags. See MANUAL for details.</li>
+ <li>Fixed an issue causing <code>bowtie2</code>’s memory usage to
+ increase over time when aligning BAM files.</li>
+ <li>Changed bowtie2 to continue flushing output in the event of a
+ partial write.</li>
+ <li>Changed the behavior of <code>bowtie2-build</code> to throw an
+ exception if it is unable to write the BWT (.1.bt2, .1.rev.bt2). In
+ prior versions <code>bowtie2-build</code>, would silently ignore the
+ error which has led some to report the absence of the BWT files in a
+ “completed” index build.</li>
+ <li>Reverted the changes made in v2.5.0 that sometimes caused unique
+ concordant alignments to be overcounted.</li>
+</ul>
+
+<h2>New Indexes for Cow, Chimp, and Rat, added to the sidebar - May 08, 2024</h2>
+<ul>
+ <li><a href="https://genome-idx.s3.amazonaws.com/bt/ARS-UCD2.0.zip"><i>B. taurus</i>, ARS-UCD2.0</a></li>
+ <li><a href="https://genome-idx.s3.amazonaws.com/bt/NHGRI_mPanTro3-v2.0.zip"><i>P. troglodytes</i>, mPanTro3-v2</a></li>
+ <li><a href="https://genome-idx.s3.amazonaws.com/bt/GRCr8.zip"><i>R. norvegicus</i>, GRCr8</a></li>
+</ul>
+
<h2>Version 2.5.3 - Jan 16, 2024</h2>
<h3 id="bowtie2">bowtie2</h3>
<ul>
=====================================
doc/website/rhsidebar.ssi
=====================================
@@ -18,10 +18,10 @@
</tr>
<tr>
<td>
- <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.5.3">Bowtie2 v2.5.3</a>
+ <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.5.4">Bowtie2 v2.5.4</a>
</td>
<td align="right">
- 01/16/24
+ 05/16/24
</td>
</tr>
<tr>
@@ -49,7 +49,7 @@
<a href="https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip"><i>H. sapiens</i>, GRCh38 no-alt analysis set</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
@@ -58,7 +58,7 @@
<a href="https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_decoy_as.zip"><i>H. sapiens</i>, GRCh38 no-alt +decoy set</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
@@ -67,7 +67,7 @@
<a href="https://genome-idx.s3.amazonaws.com/bt/grch38_1kgmaj.zip"><i>H. sapiens</i>, GRCh38 + major SNVs</a>
</td>
<td align="right">
- NCBI+1KG
+ GRC
</td>
</tr>
<tr>
@@ -80,43 +80,43 @@
<a href="https://genome-idx.s3.amazonaws.com/bt/GRCh37.zip"><i>H. sapiens</i>, GRCh37</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/Ash1v1.7.zip"><i>H. sapiens</i>, Ash1v1.7</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/chm13v2.0.zip"><i>H. sapiens</i>, CHM13 v2</a>
</td>
<td align="right">
- JHU
+ <a href="https://github.com/nanopore-wgs-consortium/CHM13">T2T</a>
</td>
</tr>
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/Ash1_v2.0.zip"><i>H. sapiens</i>, Ash1v2.0</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/chm13.draft_v1.0_plusY.zip"><i>H. sapiens</i>, CHM13 v1, plus Y</a>
</td>
<td align="right">
- JHU
+ <a href="https://github.com/nanopore-wgs-consortium/CHM13">T2T</a>
</td>
</tr>
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/chm13v2.0.zip"><i>H. sapiens</i>, CHM13 v2</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/Ash1_v2.0.zip"><i>H. sapiens</i>, Ash1v2.0</a>
</td>
<td align="right">
- <a href="https://github.com/nanopore-wgs-consortium/CHM13">T2T</a>
+ JHU
</td>
</tr>
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/chm13.draft_v1.0_plusY.zip"><i>H. sapiens</i>, CHM13 v1, plus Y</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/Ash1v1.7.zip"><i>H. sapiens</i>, Ash1v1.7</a>
</td>
<td align="right">
- <a href="https://github.com/nanopore-wgs-consortium/CHM13">T2T</a>
+ JHU
</td>
</tr>
@@ -140,19 +140,19 @@
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/GRCm38.zip"><i>M. Musculus</i>, GRCm38</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/GRCm39.zip"><i>M. Musculus</i>, GRCm39</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/GRCm39.zip"><i>M. Musculus</i>, GRCm39</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/GRCm38.zip"><i>M. Musculus</i>, GRCm38</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
@@ -174,6 +174,15 @@
</td>
</tr>
+ <tr>
+ <td>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/NHGRI_mPanTro3-v2.0.zip"><i>P. troglodytes</i>, mPanTro3-v2</a>
+ </td>
+ <td align="right">
+ NHGRI
+ </td>
+ </tr>
+
<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/Clint_PTRv2.zip"><i>P. troglodytes</i>, Clint_PTRv2</a>
@@ -203,7 +212,7 @@
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/ARS-UCD1.2.zip"><i>B. taurus</i>, ARS-UCD1.2</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/ARS-UCD2.0.zip"><i>B. taurus</i>, ARS-UCD2.0</a>
</td>
<td align="right">
NCBI
@@ -212,7 +221,7 @@
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/Sscrofa11.1.zip"><i>S. scrofa</i>, Sscrofa11.1</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/ARS-UCD1.2.zip"><i>B. taurus</i>, ARS-UCD1.2</a>
</td>
<td align="right">
NCBI
@@ -221,10 +230,10 @@
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/CanFam3.1.zip"><i>C. familiaris</i>, CanFam3.1</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/Sscrofa11.1.zip"><i>S. scrofa</i>, Sscrofa11.1</a>
</td>
<td align="right">
- Ensembl
+ NCBI
</td>
</tr>
@@ -239,10 +248,19 @@
<tr>
<td>
- <a href="https://genome-idx.s3.amazonaws.com/bt/rn4.zip"><i>R. norvegicus</i>, rn4</a>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/CanFam3.1.zip"><i>C. familiaris</i>, CanFam3.1</a>
</td>
<td align="right">
- UCSC
+ Ensembl
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/GRCr8.zip"><i>R. norvegicus</i>, GRCr8</a>
+ </td>
+ <td align="right">
+ GRC
</td>
</tr>
@@ -255,12 +273,21 @@
</td>
</tr>
+ <tr>
+ <td>
+ <a href="https://genome-idx.s3.amazonaws.com/bt/rn4.zip"><i>R. norvegicus</i>, rn4</a>
+ </td>
+ <td align="right">
+ UCSC
+ </td>
+ </tr>
+
<tr>
<td>
<a href="https://genome-idx.s3.amazonaws.com/bt/GRCg6a.zip"><i>G. gallus</i>, GRCg6a</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
@@ -278,7 +305,7 @@
<a href="https://genome-idx.s3.amazonaws.com/bt/GRCz11.zip"><i>D. rerio</i>, GRCz11</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
@@ -287,7 +314,7 @@
<a href="https://genome-idx.s3.amazonaws.com/bt/GRCz10.zip"><i>D. rerio</i>, GRCz10</a>
</td>
<td align="right">
- NCBI
+ GRC
</td>
</tr>
@@ -387,4 +414,3 @@
</ul>
</div>
</div> <!-- End of "rightside" -->
-
=====================================
filebuf.h
=====================================
@@ -951,16 +951,27 @@ private:
static void writeAsync(AsyncData *asyncDataPtr) {
AsyncData &asyncData = *asyncDataPtr;
bool abort = false;
+ size_t written = 0;
while(!abort) {
abort = asyncData.waitForBuf();
if(abort) break;
- if(asyncData.cur != fwrite((const void *)asyncData.buf, 1, asyncData.cur, asyncData.out)) {
+ while (asyncData.cur != 0) {
+ written += fwrite((const void *)(asyncData.buf + written), 1, asyncData.cur, asyncData.out);
if (errno == EPIPE) {
exit(EXIT_SUCCESS);
}
- std::cerr << "Error while flushing and closing output" << std::endl;
- throw 1;
+ if (feof(asyncData.out) || written == 0)
+ break;
+ // asyncData.buf += written;
+ asyncData.cur -= written;
+ written = 0;
}
+
+ if (written != asyncData.cur) {
+ // std::cerr << "Error while flushing and closing output" << std::endl;
+ perror("fwrite");
+ throw 1;
+ }
abort = asyncData.writeComplete();
}
=====================================
opts.h
=====================================
@@ -162,6 +162,7 @@ enum {
ARG_ALIGN_PAIRED_READS, // --align-paired-reads
ARG_SRA_ACC, // --sra-acc
ARG_SAM_APPEND_COMMENT, // --sam-append-comment
+ ARG_SAM_OPT_CONFIG, // --sam-opt-config
};
#endif
=====================================
pat.cpp
=====================================
@@ -253,9 +253,18 @@ pair<bool, int> DualPatternComposer::nextBatch(PerThreadReadBuf& pt) {
assert_eq((*srca_)[cur]->readCount(),
(*srcb_)[cur]->readCount());
}
- if(resa.second < resb.second) {
- cerr << "Error, fewer reads in file specified with -1 "
- << "than in file specified with -2" << endl;
+ if (resa.second < resb.second) {
+ cerr << "Error, fewer reads in file specified with -1 "
+ << "than in file specified with -2.";
+ if (resb.second > 0) {
+ const char *readOrigBuf = pt.bufb_[resb.second - 1].readOrigBuf.buf();
+ const char *newline = strchr(readOrigBuf, '\n');
+
+ size_t headerLength = newline - readOrigBuf;
+ string header = string(readOrigBuf, headerLength);
+ cerr << " Last successfully parsed mate: " << header << ".";
+ }
+ cerr << endl;
throw 1;
} else if(resa.second == 0 && resb.second == 0) {
ThreadSafe ts(mutex_m);
@@ -264,9 +273,19 @@ pair<bool, int> DualPatternComposer::nextBatch(PerThreadReadBuf& pt) {
}
cur = cur_; // Move on to next PatternSource
continue; // on to next pair of PatternSources
- } else if(resb.second < resa.second) {
- cerr << "Error, fewer reads in file specified with -2 "
- << "than in file specified with -1" << endl;
+ } else if (resb.second < resa.second) {
+ cerr << "Error, fewer reads in file specified with -2 "
+ << "than in file specified with -1.";
+
+ if (resa.second > 0) {
+ const char *readOrigBuf = pt.bufa_[resa.second - 1].readOrigBuf.buf();
+ const char *newline = strchr(readOrigBuf, '\n');
+
+ size_t headerLength = newline - readOrigBuf;
+ string header = string(readOrigBuf, headerLength);
+ cerr << " Last successfully parsed mate: " << header << ".";
+ }
+ cerr << endl;
throw 1;
}
assert_eq(resa.first, resb.first);
@@ -1426,7 +1445,7 @@ int BAMPatternSource::decompress_bgzf_block(uint8_t *dst, size_t dst_len, uint8_
return ret;
}
- return inflateReset(&stream);
+ return inflateEnd(&stream);
}
bool BAMPatternSource::parse(Read& ra, Read& rb, TReadId rdid) const {
=====================================
sam.h
=====================================
@@ -22,6 +22,8 @@
#include <string>
#include <vector>
+#include <string.h>
+
#include "ds.h"
#include "read.h"
#include "util.h"
@@ -157,6 +159,97 @@ public:
assert_eq(refnames_.size(), reflens_.size());
}
+ void toggleOptFlagByName(string& str) {
+ bool value = false;
+ const char *name = str.c_str();
+
+ if (str.size() < 2) {
+ cerr << "Error: " << name << " is not a valid SAM Optional flag." << endl;
+ return;
+ }
+
+ if (name[0] == '-') {
+ name += 1;
+ } else {
+ value = true;
+ }
+
+ if (strcasecmp(name, "as") == 0) {
+ print_yn_ = value;
+ } else if(strcasecmp(name, "xs") == 0) {
+ print_xs_ = value;
+ } else if(strcasecmp(name, "xss") == 0) {
+ print_xss_ = value;
+ } else if(strcasecmp(name, "yn") == 0) {
+ print_yn_ = value;
+ } else if(strcasecmp(name, "xn") == 0) {
+ print_xn_ = value;
+ } else if(strcasecmp(name, "x0") == 0) {
+ print_x0_ = value;
+ } else if(strcasecmp(name, "x1") == 0) {
+ print_x1_ = value;
+ } else if(strcasecmp(name, "xm") == 0) {
+ print_xm_ = value;
+ } else if(strcasecmp(name, "xo") == 0) {
+ print_xo_ = value;
+ } else if(strcasecmp(name, "xg") == 0) {
+ print_xg_ = value;
+ } else if(strcasecmp(name, "nm") == 0) {
+ print_nm_ = value;
+ } else if(strcasecmp(name, "md") == 0) {
+ print_md_ = value;
+ } else if(strcasecmp(name, "yf") == 0) {
+ print_yf_ = value;
+ } else if(strcasecmp(name, "yi") == 0) {
+ print_yi_ = value;
+ } else if(strcasecmp(name, "ym") == 0) {
+ print_ym_ = value;
+ } else if(strcasecmp(name, "yp") == 0) {
+ print_yp_ = value;
+ } else if(strcasecmp(name, "yt") == 0) {
+ print_yt_ = value;
+ } else if(strcasecmp(name, "ys") == 0) {
+ print_ys_ = value;
+ } else if(strcasecmp(name, "zs") == 0) {
+ print_zs_ = value;
+ } else if(strcasecmp(name, "xr") == 0) {
+ print_xr_ = value;
+ } else if(strcasecmp(name, "xt") == 0) {
+ print_xt_ = value;
+ } else if(strcasecmp(name, "xd") == 0) {
+ print_xd_ = value;
+ } else if(strcasecmp(name, "xu") == 0) {
+ print_xu_ = value;
+ } else if(strcasecmp(name, "ye") == 0) {
+ print_ye_ = value;
+ } else if(strcasecmp(name, "yl") == 0) {
+ print_yl_ = value;
+ } else if(strcasecmp(name, "yu") == 0) {
+ print_yu_ = value;
+ } else if(strcasecmp(name, "xp") == 0) {
+ print_xp_ = value;
+ } else if(strcasecmp(name, "yr") == 0) {
+ print_yr_ = value;
+ } else if(strcasecmp(name, "zb") == 0) {
+ print_zb_ = value;
+ } else if(strcasecmp(name, "zr") == 0) {
+ print_zr_ = value;
+ } else if(strcasecmp(name, "zf") == 0) {
+ print_zf_ = value;
+ } else if(strcasecmp(name, "zm") == 0) {
+ print_zm_ = value;
+ } else if(strcasecmp(name, "zi") == 0) {
+ print_zi_ = value;
+ } else if(strcasecmp(name, "zp") == 0) {
+ print_zp_ = value;
+ } else if(strcasecmp(name, "zu") == 0) {
+ print_zu_ = value;
+ } else if(strcasecmp(name, "zt") == 0) {
+ print_zt_ = value;
+ } else {
+ cerr << "Error: " << name << " is not a valid SAM Optional flag." << endl;
+ }
+ }
/**
* Print a reference name in a way that doesn't violate SAM's character
* constraints. \*|[!-()+-<>-~][!-~]*
=====================================
tokenize.h
=====================================
@@ -20,6 +20,7 @@
#ifndef TOKENIZE_H_
#define TOKENIZE_H_
+#include <ctype.h>
#include <string>
#include <sstream>
#include <limits>
@@ -40,8 +41,15 @@ static inline void tokenize(
//string::size_type lastPos = s.find_first_not_of(delims, 0);
string::size_type lastPos = 0;
string::size_type pos = s.find_first_of(delims, lastPos);
+
while (string::npos != pos || string::npos != lastPos) {
- ss.push_back(s.substr(lastPos, pos - lastPos));
+ if (pos == string::npos) {
+ pos = s.size();
+ }
+ string::size_type rtrim = pos;
+ while (isspace(s[lastPos])) lastPos++;
+ while (rtrim > 0 && isspace(s[rtrim - 1])) rtrim--;
+ ss.push_back(s.substr(lastPos, rtrim - lastPos));
lastPos = s.find_first_not_of(delims, pos);
pos = s.find_first_of(delims, lastPos);
if(ss.size() == (max - 1)) {
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/commit/5d6c8de75092d92ade6159d41a331fef13f20ebd
--
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/commit/5d6c8de75092d92ade6159d41a331fef13f20ebd
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/20240807/5807ce69/attachment-0001.htm>
More information about the debian-med-commit
mailing list