fixed issue #82

ChangeLog.md

@@ -2,6 +2,12 @@
 All notable changes to `mptp` will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.2.4] - 2018-05-14
+### Fixed
+ - If we do not manage to generate a random starting delimitation with the
+   wanted number of species (randomly chosen), we use the currently generated
+   delimitation instead.
+
 ## [0.2.3] - 2017-07-25
 ### Fixed
  - Replaced hsearch which was causing problems on APPLE with custom hashtable

README.md

@@ -78,9 +78,9 @@ where `DIR` is the directory where bash autocompletion is stored. You can use
 and the documentation, use the following commands:
 
 ```bash
-wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.3/mptp-src-0.2.3.tar.gz
-tar zxvf mptp-src-0.2.3.tar.gz
-cd mptp-src-0.2.3
+wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.4/mptp-src-0.2.4.tar.gz
+tar zxvf mptp-src-0.2.4.tar.gz
+cd mptp-src-0.2.4
 ./configure
 make
 make install  # as root, or run sudo make install
@@ -110,12 +110,12 @@ To use the pre-compiled binary, download the appropriate executable for your
 system using the following commands if you are using a Linux system:
 
 ```bash
-wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.3/mptp-0.2.3-linux-x86_64.tar.gz
-tar zxvf mptp-0.2.3-linux-x86_64.tar.gz
+wget https://github.com/Pas-Kapli/mptp/releases/download/v0.2.4/mptp-0.2.4-linux-x86_64.tar.gz
+tar zxvf mptp-0.2.4-linux-x86_64.tar.gz
 ```
 
 You will now have the binary distribution in a folder called
-`mptp-0.2.3-linux-x86_64` in which you will find three subfolders `bin`, `man`
+`mptp-0.2.4-linux-x86_64` in which you will find three subfolders `bin`, `man`
 and `doc`. We recommend making a copy or a symbolic link to the mptp binary
 `bin/mptp` in a folder included in your `$PATH`, and a copy or a symbolic link
 to the mptp man page `man/mptp.1` in a folder included in your `$MANPATH`. The

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.63])
-AC_INIT([mptp], [0.2.3], [Tomas.Flouri@h-its.org])
+AC_INIT([mptp], [0.2.4], [t.flouris@ucl.ac.uk])
 AM_INIT_AUTOMAKE([subdir-objects])
 AC_LANG([C])
 AC_CONFIG_SRCDIR([src/mptp.c])

man/mptp.1

@@ -1,6 +1,6 @@
 .\" -*- coding: utf-8 -*-
 .\" ============================================================================
-.TH mptp 1 "January 31, 2017" "mptp 0.2.2" "USER COMMANDS"
+.TH mptp 1 "May 14, 2018" "mptp 0.2.4" "USER COMMANDS"
 .\" ============================================================================
 .SH NAME
 mptp \(em single-locus species delimitation
@@ -354,5 +354,10 @@ incorrectly formatted trees.
 .TP
 .BR v0.2.3\~ "released July 25th, 2017"
 Replaced hsearch() with custom hashtable. Fixed minor output error messages.
+.TP
+.BR v0.2.4\~ "released May 14th, 2018"
+If we do not manage to generate a random starting delimitation with the wanted
+number of species (randomly chosen), we use the currently generated
+delimitation instead.
 .RE
 .LP

src/random.c

@@ -115,7 +115,14 @@ double random_delimitation(rtree_t * root,
                         root->edgelen_sum - edgelen_sum);
 
   free(inner_node_list);
-
+
+  assert(count <= species_count);
+  if (count < species_count)
+  {
+    /* TODO: This fixes issue #82, but we should implement a better, non-biased
+       way of generatng random starting delimitations */
+    species_count = count;
+  }
   assert(count == species_count);
 
   *delimited_species = species_count;