MANUAL

@@ -705,6 +705,18 @@ The query input files (specified either as `<m1>` and `<m2>`, or as
 or similar).  All quality values are assumed to be 40 on the [Phred
 quality] scale.
 
+    -F
+
+Reads are substrings (k-mers) extracted from a FASTA file `s`.
+Specifically, for every reference sequence in FASTA file `s`, Bowtie
+2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the
+end of the reference. Each k-mer is aligned as a separate read.
+Quality values are set to all Is (40 on Phred scale). Each k-mer
+(read) is given a name like `sequence`_`offset`, where `sequence`
+is the name of the FASTA sequence it was drawn from and `offset`
+is its 0-based offset of origin with respect to the sequence. Only
+single k-mers, i.e. unpaired reads, can be aligned in this way.
+
     -r
 
 The query input files (specified either as `<m1>` and `<m2>`, or as

MANUAL.markdown

@@ -767,6 +767,24 @@ The query input files (specified either as `<m1>` and `<m2>`, or as
 or similar).  All quality values are assumed to be 40 on the [Phred
 quality] scale.
 
+</td></tr><tr><td id="bowtie-options-F">
+
+[`-F`]: #bowtie-options-F
+
+    -F
+
+</td><td>
+
+Reads are substrings (k-mers) extracted from a FASTA file `s`.
+Specifically, for every reference sequence in FASTA file `s`, Bowtie
+2 aligns the k-mers at offsets 1, 1+i, 1+2i, ... until reaching the
+end of the reference. Each k-mer is aligned as a separate read.
+Quality values are set to all Is (40 on Phred scale). Each k-mer
+(read) is given a name like `sequence`_`offset`, where `sequence`
+is the name of the FASTA sequence it was drawn from and `offset`
+is its 0-based offset of origin with respect to the sequence. Only
+single k-mers, i.e. unpaired reads, can be aligned in this way.
+
 </td></tr><tr><td id="bowtie-options-r">
 
 [`-r`]: #bowtie-options-r
@@ -2425,4 +2443,3 @@ Print version information and quit.
 Print usage information and quit.
 
 </td></tr></table>
-

Makefile

@@ -420,9 +420,10 @@ doc: doc/manual.html MANUAL
 
 doc/manual.html: MANUAL.markdown
 	echo "<h1>Table of Contents</h1>" > .tmp.head
-	pandoc -T "Bowtie Manual" -B .tmp.head \
+	pandoc -B .tmp.head \
 	       --css style.css -o $@ \
 	       --from markdown --to HTML \
+	       --metadata title:"Bowtie Manual" \
 	       --table-of-contents $^
 
 MANUAL: MANUAL.markdown

NEWS

@@ -5,14 +5,15 @@ Bowtie NEWS
 
    Bowtie is now available for download.  0.9.0 is the first version to
 be released under the OSI Artistic License (see `LICENSE') and freely
-available to the public for download.  The current version is 1.2.1.1.
+available to the public for download.  The current version is 1.2.3.
 
 Reporting Issues
 ================
 
 Please report any issues using the Sourceforge bug tracker:
 
-  https://sourceforge.net/tracker/?group_id=236897&atid=1101606
+  * https://github.com/BenLangmead/bowtie/issues
+  * https://sourceforge.net/tracker/?group_id=236897&atid=1101606
 
 Announcements
 =============
@@ -26,7 +27,20 @@ subscribe to our mailing list:
 Version Release History
 =======================
 
+Version 1.2.3 - Jul 5, 2019
+    * Added support for reading and inspecting Bowtie 2 indexes.
+      Bowtie 2 indexes can now be used with either Bowtie or Bowtie 2.
+    * Added support for building an index from a gzipped-compressed
+      FASTA.
+    * Fixed issue preventing bowtie from reporting repeated alignments
+      when -M is specified.
+    * Fixed issue with -F mode omitting final base of each read.
+    * Fixed clipping of first letter of first read in batches after first.
+    * Fixed an issue preventing bowtie wrapper script from finding indexes.
+
 Version 1.2.2 - Dec 11, 2017
+Update (12/12/2017): We have had to re-release this version of bowtie to address an issue when compiling with pthreads (make NO_TBB=1).
+
     * Fixed major issue causing corrupt SAM output when using many threads (-p/--threads) on certain systems
     * Fixed major issue with incorrect alignment offsets being reported in --large-index mode
     * Fixed major issue with reads files being skipped when multiple inputs were specified together with -p/--threads

VERSION

-1.2.2
+1.2.3

blockwise_sa.h

@@ -74,7 +74,11 @@ class BlockwiseSA {
 			_logger(__logger)
 	{ }
 
-		virtual ~BlockwiseSA() { }
+		virtual ~BlockwiseSA()
+#if __cplusplus > 199711L
+			noexcept(false)
+#endif
+		{ }
 
 		/**
 		 * Get the next suffix; compute the next bucket if necessary.
@@ -200,7 +204,11 @@ class KarkkainenBlockwiseSA : public InorderBlockwiseSA<TStr> {
 #endif
 			{ _randomSrc.init(__seed); reset(); }
 
-		~KarkkainenBlockwiseSA() {
+		~KarkkainenBlockwiseSA()
+#if __cplusplus > 199711L
+			noexcept(false)
+#endif
+		{
 			if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
 			if (_done != NULL) {
 				delete[] _done;

bowtie

@@ -69,6 +69,7 @@ def main():
     bin_spec            = os.path.join(ex_path, bin_s)
 
     if args.verbose:
+        bowtie_args.append('--verbose')
         logging.getLogger().setLevel(logging.INFO)
 
     if args.large_index:
@@ -85,14 +86,16 @@ def main():
             if tot_size > small_index_max_size:
                 bin_spec = os.path.join(ex_path, bin_l)
         else:
-            if os.path.exists(args.index + idx_ext_l):
+            if not os.path.exists(arg + idx_ext_s)\
+                    and os.path.exists(args.index + idx_ext_l):
                 bin_spec = os.path.join(ex_path, bin_l)
         bowtie_args.insert(0, args.index)
     else:
         for arg in bowtie_args:
             if arg[0] == '-':
                 continue
-            if os.path.exists(arg + idx_ext_l):
+            if not os.path.exists(arg + idx_ext_s)\
+                    and os.path.exists(arg + idx_ext_l):
                 bin_spec = os.path.join(ex_path, bin_l)
 
     if args.debug:

bowtie-inspect

@@ -34,8 +34,8 @@ def main():
     inspect_bin_name      = "bowtie-inspect"
     inspect_bin_s         = "bowtie-inspect-s"
     inspect_bin_l         = "bowtie-inspect-l"
-    idx_ext_l             = '.1.ebwtl'; 
-    idx_ext_s             = '.1.ebwt'; 
+    idx_ext_l             = '.1.ebwtl'
+    idx_ext_s             = '.1.ebwt'
     curr_script           = os.path.realpath(inspect.getsourcefile(main))
     ex_path               = os.path.dirname(curr_script)
     inspect_bin_spec      = os.path.join(ex_path,inspect_bin_s)
@@ -43,6 +43,7 @@ def main():
     options,arguments     = bld.build_args()
 
     if '--verbose' in options:
+        arguments.append('--verbose')
         logging.getLogger().setLevel(logging.INFO)
 
     if '--debug' in options:
@@ -68,8 +69,3 @@ def main():
 
 if __name__ == "__main__":
     main()
-
-
-
-
-

debian/changelog

+bowtie (1.2.3+dfsg-1) unstable; urgency=medium
+
+  [ Andreas Tille ]
+  * Fix edam syntax input+output is singular
+
+  [ Alexandre Mestiashvili ]
+  * New upstream version 1.2.3+dfsg
+  * Drop applied by upstream and refresh patches
+  * Add strip_html5shiv.patch, removing condition loading html5shiv for old IEs
+  * Update d/control, remove version from seqan-dev, bump Policy to 4.4.0
+  * Switch to debhelper-compat, drop d/compat
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 11 Jul 2019 16:09:02 +0200
+
 bowtie (1.2.2+dfsg-4) unstable; urgency=medium
 
   [ Andreas Tille ]

debian/compat

-11

debian/control

@@ -7,13 +7,13 @@ Uploaders: Steffen Moeller <moeller@debian.org>,
            Alexandre Mestiashvili <mestia@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper-compat (= 12),
                help2man,
                libtbb-dev,
                python,
-               seqan-dev (>= 1.4),
+               seqan-dev,
                zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie
 Vcs-Git: https://salsa.debian.org/med-team/bowtie.git
 Homepage: http://bowtie-bio.sourceforge.net/

debian/patches/fix_isa_return.patch

-Subject: Fix isa return type
-From: ch4rr0
-Comment:
- see https://github.com/BenLangmead/bowtie/commit/58c6ac97b1938909881877ef83167f5eff0e8ab1
---- bowtie.orig/ebwt.h
-+++ bowtie/ebwt.h
-@@ -862,7 +862,7 @@
- 	TIndexOffU*   ftab() const         { return _ftab; }
- 	TIndexOffU*   eftab() const        { return _eftab; }
- 	TIndexOffU*   offs() const         { return _offs; }
--	uint32_t*   isa() const          { return _isa; } /* check */
-+	TIndexOffU*   isa() const          { return _isa; } /* check */
- 	TIndexOffU*   plen() const         { return _plen; }
- 	TIndexOffU*   rstarts() const      { return _rstarts; }
- 	uint8_t*    ebwt() const         { return _ebwt; }

debian/patches/seqan-rename-ChunkPool.patch

@@ -232,7 +232,7 @@ Last-Update: 2013-04-18
  	chunkVerbose			= false; // have chunk allocator output status messages?
  	useV1					= true;
  	reportSe				= false;
-@@ -1340,7 +1340,7 @@
+@@ -1343,7 +1343,7 @@
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
  
@@ -241,7 +241,7 @@ Last-Update: 2013-04-18
  	UnpairedExactAlignerV1Factory alSEfact(
  			ebwt,
  			NULL,
-@@ -1631,7 +1631,7 @@
+@@ -1632,7 +1632,7 @@
  	// Global initialization
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
@@ -250,7 +250,7 @@ Last-Update: 2013-04-18
  
  	Unpaired1mmAlignerV1Factory alSEfact(
  			ebwtFw,
-@@ -2084,7 +2084,7 @@
+@@ -2083,7 +2083,7 @@
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);
  
@@ -259,7 +259,7 @@ Last-Update: 2013-04-18
  	Unpaired23mmAlignerV1Factory alSEfact(
  			ebwtFw,
  			&ebwtBw,
-@@ -2756,7 +2756,7 @@
+@@ -2753,7 +2753,7 @@
  	// Global initialization
  	PatternSourcePerThreadFactory* patsrcFact = createPatsrcFactory(_patsrc, tid, readsPerBatch);
  	HitSinkPerThreadFactory* sinkFact = createSinkFactory(_sink, tid);

debian/patches/seqan-rename-fill-to-resize.patch

@@ -54,7 +54,7 @@ Last-Update: 2014-08-13
  			Timer timer(cout, "  Ranking v-sort output time: ", this->verbose());
 --- bowtie.orig/blockwise_sa.h
 +++ bowtie/blockwise_sa.h
-@@ -665,8 +665,8 @@
+@@ -673,8 +673,8 @@
  					try {
  						// Allocate and initialize containers for holding bucket
  						// sizes and representatives.
@@ -65,7 +65,7 @@ Last-Update: 2014-08-13
  					} catch(bad_alloc &e) {
  						if(this->_passMemExc) {
  							throw e; // rethrow immediately
-@@ -1055,7 +1055,7 @@
+@@ -1063,7 +1063,7 @@
  				hi = _sampleSuffs[cur_block];
  				//zHi.resizeExact(_dcV);
  				//zHi.fillZero();
@@ -74,7 +74,7 @@ Last-Update: 2014-08-13
  				assert_eq(getValue(zHi, 0), 0);
  				calcZ(t, hi, zHi, this->verbose(), this->sanityCheck());
  			}
-@@ -1066,7 +1066,7 @@
+@@ -1074,7 +1074,7 @@
  				lo = _sampleSuffs[cur_block-1];
  				//zLo.resizeExact(_dcV);
  				//zLo.fillZero();

debian/patches/series

-fix_isa_return.patch
+strip_html5shiv.patch
+spelling.patch
 no_hash_style_both_for_mips.patch
 use-dpkg-buildflags.patch
 use_debian_seqan.patch
@@ -11,7 +12,6 @@ seqan-popcount.patch
 bowtie_ContextLss-1.1-1.4.patch
 ppc64el.patch
 enable_arm64.patch
-spelling.patch
 reproducible.patch
 gcc-64bit.patch
 build-as-Cpp03.patch

debian/patches/spelling.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 01 Oct 2015 09:47:23 +0200
+Author: Alex Mestiashvili <mestia@debian.org>
+Last-Update: Thu, 11 Jul 2019 14:42:23 +0200
 Description: Fix spelling
-
+--- bowtie.orig/ref_read.cpp
++++ bowtie/ref_read.cpp
+@@ -263,7 +263,7 @@
+ 				     << "reference into smaller chunks and index each independently." << endl;
+ #else
+ 				cerr << "Error: Reference sequence has more than 2^32-1 characters!  Please try to" << endl
+-				     << "build a large index instead using the appropiate options." << endl;
++				     << "build a large index instead using the appropriate options." << endl;
+ #endif
+ 				throw 1;
+ 			}
 --- bowtie.orig/MANUAL
 +++ bowtie/MANUAL
 @@ -543,7 +543,7 @@
@@ -13,6 +23,35 @@ Description: Fix spelling
  
  It is recommended that you always run the bowtie wrappers and not run
  the binaries directly.
+--- bowtie.orig/doc/website/manual.ssi
++++ bowtie/doc/website/manual.ssi
+@@ -190,7 +190,7 @@
+ <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p>
+ <p>Note that SOLiD-generated read files can have “orphaned” mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]’s conversion tool (click “NGS: QC and manipulation”, then “SOLiD-to-FASTQ” in the left-hand sidebar).</p>
+ <h2 id="wrapper-scripts">Wrapper scripts</h2>
+-<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between “small” and “large” index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p>
++<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between “small” and “large” index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p>
+ <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p>
+ <h2 id="small-and-large-indexes">Small and large indexes</h2>
+ <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a “small” index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a “large” index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p>
+@@ -1251,4 +1251,4 @@
+ <p>Print usage information and quit.</p>
+ </td>
+ </tr>
+-</table>
+\ No newline at end of file
++</table>
+--- bowtie.orig/doc/manual.html
++++ bowtie/doc/manual.html
+@@ -210,7 +210,7 @@
+ <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p>
+ <p>Note that SOLiD-generated read files can have “orphaned” mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]’s conversion tool (click “NGS: QC and manipulation”, then “SOLiD-to-FASTQ” in the left-hand sidebar).</p>
+ <h2 id="wrapper-scripts">Wrapper scripts</h2>
+-<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between “small” and “large” index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p>
++<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between “small” and “large” index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p>
+ <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p>
+ <h2 id="small-and-large-indexes">Small and large indexes</h2>
+ <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a “small” index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a “large” index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p>
 --- bowtie.orig/MANUAL.markdown
 +++ bowtie/MANUAL.markdown
 @@ -558,7 +558,7 @@
@@ -24,45 +63,3 @@ Description: Fix spelling
  
  It is recommended that you always run the bowtie wrappers and not run
  the binaries directly.
---- bowtie.orig/doc/manual.html
-+++ bowtie/doc/manual.html
-@@ -199,7 +199,7 @@
- <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p>
- <p>Note that SOLiD-generated read files can have &quot;orphaned&quot; mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click &quot;NGS: QC and manipulation&quot;, then &quot;SOLiD-to-FASTQ&quot; in the left-hand sidebar).</p>
- <h2 id="wrapper-scripts">Wrapper scripts</h2>
--<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between &quot;small&quot; and &quot;large&quot; index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p>
-+<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between &quot;small&quot; and &quot;large&quot; index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p>
- <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p>
- <h2 id="small-and-large-indexes">Small and large indexes</h2>
- <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a &quot;small&quot; index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a &quot;large&quot; index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p>
---- bowtie.orig/ref_read.cpp
-+++ bowtie/ref_read.cpp
-@@ -263,7 +263,7 @@
- 				     << "reference into smaller chunks and index each independently." << endl;
- #else
- 				cerr << "Error: Reference sequence has more than 2^32-1 characters!  Please try to" << endl
--				     << "build a large index instead using the appropiate options." << endl;
-+				     << "build a large index instead using the appropriate options." << endl;
- #endif
- 				throw 1;
- 			}
---- bowtie.orig/shmem.h
-+++ bowtie/shmem.h
-@@ -67,7 +67,7 @@
- 				cerr << "EEXIST" << endl;
- 			} else if(errno == EINVAL) {
- 				cerr << "Warning: shared-memory chunk's segment size doesn't match expected size (" << (shmemLen) << ")" << endl
--					 << "Deleteing old shared memory block and trying again." << endl;
-+					 << "Deleting old shared memory block and trying again." << endl;
- 				shmid = shmget(key, 0, 0);
- 				if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
- 					cerr << "shmctl returned " << ret
-@@ -105,7 +105,7 @@
- 		if(ds.shm_segsz != shmemLen) {
- 			cerr << "Warning: shared-memory chunk's segment size (" << ds.shm_segsz
- 				 << ") doesn't match expected size (" << shmemLen << ")" << endl
--				 << "Deleteing old shared memory block and trying again." << endl;
-+				 << "Deleting old shared memory block and trying again." << endl;
- 			if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
- 				cerr << "shmctl returned " << ret << " for IPC_RMID and errno is " << errno << endl;
- 				throw 1;

debian/patches/strip_html5shiv.patch

+Subject: Strip IE related condition to make lintian happy
+ we don't care about ancient versions of IE
+From: Alex Mestiashvili <mestia@debian.org>
+Forwarded: no
+--- bowtie.orig/doc/manual.html
++++ bowtie/doc/manual.html
+@@ -12,9 +12,6 @@
+       div.column{display: inline-block; vertical-align: top; width: 50%;}
+   </style>
+   <link rel="stylesheet" href="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>

doc/website/latest-version.txt

-0.12.8
+i.2.3