update authors list + improve description of --wrtsize

AUTHORS

@@ -1,2 +1,5 @@
+Authors are listed in alphabetical order (more details in the manual):
+Chaoxing Dai
 Timothée Flutre
 Xiaoquan Wen
+Gao Wang

NEWS

@@ -1,8 +1,9 @@
-2015-07-16 v1.3.1a
+2015-08-02 v1.3.1b
 ==================
 
 Performance improvements
 * implement the SQUAREM procedure to speed-um 'eqtlbma_hm' (thanks to C. Dai)
+* reduce memory requirement of 'eqtlbma_bf' (thanks to G. Wang)
 
 Bug fixes
 * filter properly SNPs with low MAF when provided in "custom" format (thanks to

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([eqtlbma], [1.3.1a], [eqtlbma-users@googlegroups.com], [eqtlbma], [https://github.com/timflutre/eqtlbma/wiki])
+AC_INIT([eqtlbma], [1.3.1b], [eqtlbma-users@googlegroups.com], [eqtlbma], [https://github.com/timflutre/eqtlbma/wiki])
 AC_CONFIG_SRCDIR([src/eqtlbma_bf.cpp]) # safety check
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])

doc/manual_eqtlbma.texi

@@ -15,7 +15,7 @@
 This manual is for eQtlBma (version @value{VERSION}, @value{UPDATED}),
 which implements Bayesian methods for eQTL detection.
 
-Copyright @copyright{} 2012-2015 Timoth@'ee Flutre, Xiaoquan Wen.
+Copyright @copyright{} 2012-2015 eQtlBma authors.
 
 @quotation
 Permission is granted to copy, distribute and/or modify this document
@@ -40,7 +40,7 @@ supports it in developing GNU and promoting software freedom.''
 @titlepage
 @title eQtlBma
 @subtitle for version @value{VERSION}, @value{UPDATED}
-@author T. Flutre and X. Wen (@email{eqtlbma-users@@googlegroups.com})
+@author eQtlBma authors (@email{eqtlbma-users@@googlegroups.com})
 @page
 @vskip 0pt plus 1filll
 @insertcopying
@@ -588,9 +588,10 @@ At some point we will have to improve the code to also handle the strand, if spe
 The option @option{--out} requires a character string which will be used as a prefix to name the output files.
 Moreover, all output files are directly written in a compressed mode using @url{http://www.zlib.net/,zlib}.
 That is, all output files are readable by @command{gzip} and @command{zcat}.
-The option @option{--wrtsize} controls the amount of output at a time.
+
+Moreover, the option @option{--wrtsize} controls the amount of output at a time.
 It requires a positive integer, which specifies how many genes to analyze before their results are written to disk and released from memory.
-This option prevents @command{eqtlbma_bf} from using too much memory if there are large number of cis SNPs per gene.
+This option prevents @command{eqtlbma_bf} from using too much memory if there are many @emph{cis} SNPs per gene.
 
 The program @command{eqtlbma_bf} can perform several analyzes.
 The option @option{--analys sep} means that the gene-SNP pairs will be tested for association using the subgroup-by-subgroup analysis (``separate'' analysis).
@@ -1085,6 +1086,7 @@ Xiaoquan (William) Wen wrote the C++ class that computes the multivariate approx
 The SQUAREM procedure was implemented thanks to the help of Chaoxing Dai.
 
 Gao Wang fixed a bug when filtering SNPs with missing genotypes when provided in the ``custom'' format.
+He also reduced memory requirement of @command{eqtlbma_bf} by adding @option{--wrtsize}.
 
 Sarah Urbut provided useful feedback at various time points.
 

src/eqtlbma_bf.cpp

@@ -1,7 +1,7 @@
 /** \file eqtlbma_bf.cpp
  *
  *  `eqtlbma_bf' performs eQTL mapping in multiple subgroups via a Bayesian model.
- *  Copyright (C) 2012-2014 Timothée Flutre
+ *  Copyright (C) 2012-2015 Timothée Flutre
  *
  *  This program is free software: you can redistribute it and/or modify
  *  it under the terms of the GNU General Public License as published by
@@ -195,9 +195,9 @@ void help(char ** argv)
        << "      --sbgrp\tidentifier of the subgroup to analyze" << endl
        << "\t\tuseful for quick analysis and debugging" << endl
        << "\t\tcan be 'sbgrp1+sbgrp3' for instance" << endl
-       << "      --wrtsize\tsize (number of genes) per write to output file (default=10)" << endl
-       << "\t\tset to smaller size when each gene has large number of cis SNPs" << endl
+       << "      --wrtsize\tnumber of genes which results are written at once (default=10)" << endl
        << "\t\tto prevent excessive memory usage" << endl
+       << "\t\ttune it depending on the average number of cis SNPs per gene" << endl
        << endl;
 }