VSEARCH 2.10.4: Fixes x86_64 SIMD alignment bug and others

LICENSE.txt

@@ -1,6 +1,6 @@
   VSEARCH: a versatile open source tool for metagenomics
 
-  Copyright (C) 2014-2018, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
+  Copyright (C) 2014-2019, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
   All rights reserved.
 
   Contact: Torbjorn Rognes <[email protected]>,

README.md

@@ -24,7 +24,7 @@ Most of the nucleotide based commands and options in USEARCH version 7 are suppo
 
 ## Getting Help
 
-If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.
+If you can't find an answer in the [VSEARCH documentation](https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch_manual.pdf), please visit the [VSEARCH Web Forum](https://groups.google.com/forum/#!forum/vsearch-forum) to post a question or start a discussion.
 
 ## Example
 
@@ -37,9 +37,9 @@ In the example below, VSEARCH will identify sequences in the file database.fsa t
 **Source distribution** To download the source distribution from a [release](https://github.com/torognes/vsearch/releases) and build the executable and the documentation, use the following commands:
 
 ```
-wget https://github.com/torognes/vsearch/archive/v2.10.3.tar.gz
-tar xzf v2.10.3.tar.gz
-cd vsearch-2.10.3
+wget https://github.com/torognes/vsearch/archive/v2.10.4.tar.gz
+tar xzf v2.10.4.tar.gz
+cd vsearch-2.10.4
 ./autogen.sh
 ./configure
 make
@@ -68,43 +68,43 @@ Binary distributions are provided for x86-64 systems running GNU/Linux, macOS (v
 Download the appropriate executable for your system using the following commands if you are using a Linux x86_64 system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch-2.10.3-linux-x86_64.tar.gz
-tar xzf vsearch-2.10.3-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-linux-x86_64.tar.gz
+tar xzf vsearch-2.10.4-linux-x86_64.tar.gz
 ```
 
 Or these commands if you are using a Linux ppc64le system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch-2.10.3-linux-ppc64le.tar.gz
-tar xzf vsearch-2.10.3-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-linux-ppc64le.tar.gz
+tar xzf vsearch-2.10.4-linux-ppc64le.tar.gz
 ```
 
 Or these commands if you are using a Linux aarch64 system:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch-2.10.3-linux-aarch64.tar.gz
-tar xzf vsearch-2.10.3-linux-aarch64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-linux-aarch64.tar.gz
+tar xzf vsearch-2.10.4-linux-aarch64.tar.gz
 ```
 
 Or these commands if you are using a Mac:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch-2.10.3-macos-x86_64.tar.gz
-tar xzf vsearch-2.10.3-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-macos-x86_64.tar.gz
+tar xzf vsearch-2.10.4-macos-x86_64.tar.gz
 ```
 
 Or if you are using Windows, download and extract (unzip) the contents of this file:
 
 ```
-https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch-2.10.3-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch-2.10.4-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.10.3-linux-x86_64` or `vsearch-2.10.3-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`.
+Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.10.4-linux-x86_64` or `vsearch-2.10.4-macos-x86_64` in which you will find three subfolders `bin`, `man` and `doc`. We recommend making a copy or a symbolic link to the vsearch binary `bin/vsearch` in a folder included in your `$PATH`, and a copy or a symbolic link to the vsearch man page `man/vsearch.1` in a folder included in your `$MANPATH`. The PDF version of the manual is available in `doc/vsearch_manual.pdf`.
 
-Windows: You will now have the binary distribution in a folder called `vsearch-2.10.3-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`.
+Windows: You will now have the binary distribution in a folder called `vsearch-2.10.4-win-x86_64`. The vsearch executable is called `vsearch.exe`. The manual in PDF format is called `vsearch_manual.pdf`.
 
 
-**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.10.3/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.10.4/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
 
 
 ## Plugins, packages, and wrappers

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([vsearch], [2.10.3], [[email protected]])
+AC_INIT([vsearch], [2.10.4], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "December 19, 2018" "version 2.10.3" "USER COMMANDS"
+.TH vsearch 1 "January 4, 2019" "version 2.10.4" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication and
@@ -3500,6 +3500,12 @@ Fixed bug in sintax with reversed order of domain and kingdom.
 .BR v2.10.3\~ "released December 19th, 2018"
 Ported to Linux on ARMv8 (aarch64). Fixed compilation warning with gcc
 version 8.1.0 and 8.2.0.
+.TP
+.BR v2.10.4\~ "released January 4th, 2019"
+Fixed serious bug in x86_64 SIMD alignment code introduced in version
+2.10.3. Added link to BioConda in README. Fixed bug in fastq_stats
+with sequence length 1. Fixed use of equals symbol in UC files for
+identical sequences with cluster_fast.
 .RE
 .LP
 .\" ============================================================================

src/align_simd.cc

@@ -2,7 +2,7 @@
 
   VSEARCH: a versatile open source tool for metagenomics
 
-  Copyright (C) 2014-2018, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
+  Copyright (C) 2014-2019, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
   All rights reserved.
 
   Contact: Torbjorn Rognes <[email protected]>,
@@ -162,7 +162,7 @@ const uint16x8_t neon_mask =
 typedef __m128i VECTOR_SHORT;
 
 #define v_init(a,b,c,d,e,f,g,h) _mm_set_epi16(h,g,f,e,d,c,b,a)
-#define v_load(a) _mm_load_si128((VECTOR_SHORT *)a)
+#define v_load(a) _mm_load_si128((VECTOR_SHORT *)(a))
 #define v_store(a, b) _mm_store_si128((VECTOR_SHORT *)(a), (b))
 #define v_merge_lo_16(a, b) _mm_unpacklo_epi16((a),(b))
 #define v_merge_hi_16(a, b) _mm_unpackhi_epi16((a),(b))

src/results.cc

@@ -2,7 +2,7 @@
 
   VSEARCH: a versatile open source tool for metagenomics
 
-  Copyright (C) 2014-2018, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
+  Copyright (C) 2014-2019, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
   All rights reserved.
 
   Contact: Torbjorn Rognes <[email protected]>,
@@ -197,15 +197,28 @@ void results_show_uc_one(FILE * fp,
     strand: + or -
     0
     0
-    compressed alignment, e.g. 9I92M14D, or "=" if prefect alignment
+    compressed alignment, e.g. 9I92M14D, or "=" if perfect alignment
     query label
     target label
   */
 
   if (hp)
     {
-      bool perfect = (hp->matches == qseqlen) &&
-        ((uint64_t)(qseqlen) == db_getsequencelen(hp->target));
+      bool perfect;
+
+      if (opt_cluster_fast)
+        {
+          /* cluster_fast */
+          /* use = for identical sequences ignoring terminal gaps */
+          perfect = (hp->matches == hp->internal_alignmentlength);
+        }
+      else
+        {
+          /* cluster_size, cluster_smallmem, cluster_unoise */
+          /* usearch_global, search_exact, allpairs_global */
+          /* use = for strictly identical sequences */
+          perfect = (hp->matches == hp->nwalignmentlength);
+        }
 
       fprintf(fp,
               "H\t%d\t%" PRId64 "\t%.1f\t%c\t0\t0\t%s\t%s\t%s\n",