VSEARCH 2.8.3: Fix segfault bug for derep_fulllength with uc

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/v2.8.2/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/v2.8.3/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.
 
 ## 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/v2.8.2.tar.gz
-tar xzf v2.8.2.tar.gz
-cd vsearch-2.8.2
+wget https://github.com/torognes/vsearch/archive/v2.8.3.tar.gz
+tar xzf v2.8.3.tar.gz
+cd vsearch-2.8.3
 ./autogen.sh
 ./configure
 make
@@ -70,36 +70,36 @@ 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/v2.8.2/vsearch-2.8.2-linux-x86_64.tar.gz
-tar xzf vsearch-2.8.2-linux-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.8.3/vsearch-2.8.3-linux-x86_64.tar.gz
+tar xzf vsearch-2.8.3-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/v2.8.2/vsearch-2.8.2-linux-ppc64le.tar.gz
-tar xzf vsearch-2.8.2-linux-ppc64le.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.8.3/vsearch-2.8.3-linux-ppc64le.tar.gz
+tar xzf vsearch-2.8.3-linux-ppc64le.tar.gz
 ```
 
 Or these commands if you are using a Mac:
 
 ```sh
-wget https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch-2.8.2-macos-x86_64.tar.gz
-tar xzf vsearch-2.8.2-macos-x86_64.tar.gz
+wget https://github.com/torognes/vsearch/releases/download/v2.8.3/vsearch-2.8.3-macos-x86_64.tar.gz
+tar xzf vsearch-2.8.3-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/v2.8.2/vsearch-2.8.2-win-x86_64.zip
+https://github.com/torognes/vsearch/releases/download/v2.8.3/vsearch-2.8.3-win-x86_64.zip
 ```
 
-Linux and Mac: You will now have the binary distribution in a folder called `vsearch-2.8.2-linux-x86_64` or `vsearch-2.8.2-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-2.8.3-linux-x86_64` or `vsearch-2.8.3-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`.
 
-Windows: You will now have the binary distribution in a folder called `vsearch-2.8.2-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-2.8.3-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/v2.8.2/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 `$MANPATH`. The manual in both formats is also available with the binary distribution. The manual in PDF form ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.2/vsearch_manual.pdf)) is also attached to the latest [release](https://github.com/torognes/vsearch/releases).
+**Documentation** The VSEARCH user's manual is available in the `man` folder in the form of a [man page](https://github.com/torognes/vsearch/blob/master/man/vsearch.1). A pdf version ([vsearch_manual.pdf](https://github.com/torognes/vsearch/releases/download/v2.8.3/vsearch_manual.pdf)) will be generated by `make`. To install the manpage manually, copy the `vsearch.1` file or a create a symbolic link to `vsearch.1` in a folder included in your `$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/v2.8.3/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], [2.8.2], [[email protected]])
+AC_INIT([vsearch], [2.8.3], [[email protected]])
 AC_CANONICAL_TARGET
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C++])

man/vsearch.1

@@ -1,5 +1,5 @@
 .\" ============================================================================
-.TH vsearch 1 "August 21, 2018" "version 2.8.2" "USER COMMANDS"
+.TH vsearch 1 "August 31, 2018" "version 2.8.3" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 vsearch \(em chimera detection, clustering, dereplication and
@@ -3406,6 +3406,9 @@ for full-length dereplication in cases with many duplicate sequences.
 Improved wording of fastq_mergepairs report. Updated manual regarding
 use of sizein and sizeout with dereplication. Changed a compiler
 option.
+.TP
+.BR v2.8.3\~ "released August 31st, 2018"
+Fix for segmentation fault for \-\-derep_fulllength with \-\-uc.
 .RE
 .LP
 .\" ============================================================================

src/derep.cc

@@ -257,6 +257,15 @@ void derep_fulllength()
   const unsigned int terminal = (unsigned int)(-1);
   memset(nextseqtab, terminal, sizeof(unsigned int) * alloc_seqs);
 
+  /* alloc and init table of pointers to the headers */
+
+  char ** headertab = 0;
+  if (opt_uc)
+    {
+      headertab = (char **) xmalloc(sizeof(char*) * alloc_seqs);
+      memset(headertab, 0, sizeof(char*) * alloc_seqs);
+    }
+
   show_rusage();
 
   char * match_strand = (char *) xmalloc(alloc_seqs);
@@ -329,6 +338,13 @@ void derep_fulllength()
                  terminal,
                  sizeof(unsigned int) * alloc_seqs);
 
+          if (opt_uc)
+            {
+              headertab = (char**) xrealloc(headertab,
+                                            sizeof(char*) * new_alloc_seqs);
+              memset(headertab + alloc_seqs, 0, sizeof(char*) * alloc_seqs);
+            }
+
           match_strand = (char *) xrealloc(match_strand, new_alloc_seqs);
           memset(match_strand + alloc_seqs, 0, alloc_seqs);
 
@@ -406,6 +422,7 @@ void derep_fulllength()
             }
         }
 
+      char * header = fastx_get_header(h);
       int abundance = fastx_get_abundance(h);
       int64_t ab = opt_sizein ? abundance : 1;
       sumsize += ab;
@@ -417,12 +434,12 @@ void derep_fulllength()
           unsigned int last = bp->seqno_last;
           nextseqtab[last] = sequencecount;
           bp->seqno_last = sequencecount;
+          if (opt_uc)
+            headertab[sequencecount] = xstrdup(header);
         }
       else
         {
           /* no identical sequences yet */
-          char * header = fastx_get_header(h);
-
           bp->size = ab;
           bp->hash = hash;
           bp->seqno_first = sequencecount;
@@ -631,7 +648,7 @@ void derep_fulllength()
                     "H\t%" PRId64 "\t%" PRId64 "\t%.1f\t%s\t0\t0\t*\t%s\t%s\n",
                     i, len, 100.0,
                     (match_strand[next] ? "-" : "+"),
-                    db_getheader(next), h);
+                    headertab[next], h);
 
           progress_update(i);
         }
@@ -682,6 +699,14 @@ void derep_fulllength()
         }
     }
 
+  if (opt_uc)
+    {
+      for (uint64_t i=0; i<alloc_seqs; i++)
+        if (headertab[i])
+          xfree(headertab[i]);
+      xfree(headertab);
+    }
+
   show_rusage();
 
   xfree(match_strand);