diff --git a/AUTHORS b/AUTHORS index eeb64b6..7791f42 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,2 +1,5 @@ +Authors are listed in alphabetical order (more details in the manual): +Chaoxing Dai Timothée Flutre Xiaoquan Wen +Gao Wang diff --git a/NEWS b/NEWS index 89d1899..988fce2 100644 --- a/NEWS +++ b/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 diff --git a/configure.ac b/configure.ac index 7da9b68..831b2cc 100644 --- a/configure.ac +++ b/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]) diff --git a/doc/manual_eqtlbma.pdf b/doc/manual_eqtlbma.pdf index c946a0d..fdf00ca 100644 Binary files a/doc/manual_eqtlbma.pdf and b/doc/manual_eqtlbma.pdf differ diff --git a/doc/manual_eqtlbma.texi b/doc/manual_eqtlbma.texi index f4723ba..b517376 100644 --- a/doc/manual_eqtlbma.texi +++ b/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. diff --git a/src/eqtlbma_bf.cpp b/src/eqtlbma_bf.cpp index 18c3234..02de371 100644 --- a/src/eqtlbma_bf.cpp +++ b/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; }