Scripts prepared for version 1.0

README

@@ -8,7 +8,7 @@ It uses parallel computing technologies such as OpenMP in order to reduce the pr
 It contains three binaries:
 * hpg-var-effect retrieves the effect of genome variations.
 * hpg-var-gwas conducts genomic-wide association analysis such as chi-square and Fisher's exact test, and family-based analysis such as transmission disequilibrium test (TDT).,
-* hpg-var-vcf allows one to preprocess files containing genome variations in Variant Call Format.
+* hpg-var-vcf allows to preprocess files containing genome variations in Variant Call Format. Filtering, merging, splitting and retrieving statistics are the features currently implemented.
 
 
 CONTENTS

SConstruct

@@ -51,7 +51,7 @@ t = SConscript("test/SConscript", exports = ['env', 'debug', 'commons_path', 'bi
 # For the packaging manager: Don't forget to point the XXX_INCLUDE_PATH and XXX_LIBRARY_PATH 
 # variables to the application libraries folder!!
 tb = env.Package(NAME          = 'hpg-variant',
-                VERSION        = '0.99.4',
+                VERSION        = '1.0',
                 PACKAGEVERSION = 0,
                 PACKAGETYPE    = 'src_targz',
                 source         = env.FindSourceFiles() + env.FindHeaderFiles(progs) + 

deb/SConscript

@@ -4,7 +4,7 @@ Import('env') # exported by parent SConstruct
 
 # Here's the core info for the DEBIAN/control file of the package
 DEBNAME = "hpg-variant"
-DEBVERSION = "0.99.4"
+DEBVERSION = "1.0"
 DEBMAINT = "Cristina Yenyxe Gonzalez Garcia <[email protected]>"
 DEBARCH = "amd64"
 DEBDEPENDS = "libc6, libcurl4-openssl-dev, libgsl0ldbl, libxml2, zlib1g"
@@ -18,8 +18,9 @@ DEBDESC = ''.join([ "Bioinformatics tool suite for analyzing genomic variations\
 "  * hpg-var-gwas conducts genomic-wide association analysis such as chi-square\n",
 "    and Fisher's exact test, and family-based analysis such as transmission\n",
 "    disequilibrium test (TDT).\n",
-"  * hpg-var-vcf allows one to preprocess files containing genome variations in\n",
-"    Variant Call Format." ])
+"  * hpg-var-vcf allows to preprocess files containing genome variations in\n",
+"    Variant Call Format. Filtering, merging, splitting and retrieving \n"
+"    statistics are the features currently implemented." ])
 
 DEBFILES = [
     # Now we specify the files to be included in the .deb

rpm/SConscript

@@ -3,14 +3,14 @@ import hashlib, os, shutil, sys
 Import('env') # exported by parent SConstruct
 
 RPMNAME = "hpg-variant"
-RPMVERSION = "0.99.4"
+RPMVERSION = "1.0"
 RPMARCH = "x86_64"
 RPMBUILDREQUIRES = "gcc glibc-devel scons libcurl-devel gsl-devel libxml2-devel ncurses-devel zlib-devel".split(" ")
 RPMREQUIRES = "libcurl gsl libxml2 zlib".split(" ") # what are we dependent on?
-RPMSUMMARY = "HPG Variant summary"
+RPMSUMMARY = "HPG Variant is a suite for the study of genomic variations"
 RPMDESC = "HPG Variant retrieves the effect of genome mutations and allows to conduct analysis"
 RPMSECTION = "Application/Engineering"
-RPMSOURCE = "hpg-variant-0.99.4.tar.gz"
+RPMSOURCE = "hpg-variant-1.0.tar.gz"
 RPMURL = "http://bioinfo.cipf.es"
 
 RPMBUILDIR = 'rpmbuild'

rpm/hpg-variant.spec

@@ -1,5 +1,5 @@
 %define name hpg-variant
-%define version 0.99.4
+%define version 1.0
 Name:           %{name}
 Version:        %{version}
 Release:        1%{?dist}
@@ -32,8 +32,9 @@ It contains three binaries:
 * hpg-var-gwas conducts genomic-wide association analysis such as chi-square 
   and Fisher's exact test, and family-based analysis such as transmission 
   disequilibrium test (TDT).
-* hpg-var-vcf allows one to preprocess files containing genome variations in 
-  Variant Call Format.
+* hpg-var-vcf allows to preprocess files containing genome variations in 
+  Variant Call Format. Filtering, merging, splitting and retrieving statistics 
+  are the features currently implemented.
 
 %prep
 %setup -q
@@ -68,6 +69,13 @@ cp bin/bash_completion/hpg-var-vcf %{buildroot}%{_sysconfdir}/bash_completion.d/
 
 
 %changelog
+* Thu Nov 07 2013 Cristina Yenyxe Gonzalez <[email protected]> - 1.0
+- Support for multigenerational families in PED files
+- Merge tool notifies when files are unsorted
+- All tools notify when output files can't be created
+- Sample statistics added to database generated by hpg-var-vcf stats
+- Logging output redirection: DEBUG/INFO to stdout, WARN/ERROR/FATAL to stderr
+
 * Wed Sep 18 2013 Cristina Yenyxe Gonzalez <[email protected]> - 0.99.4
 - Great reduction of memory usage in the VCF merging tool allows to merge 
   hundreds of VCF files at twice the previous speed

src/hpg_variant_utils.c

@@ -321,7 +321,7 @@ void show_usage(char *tool, void **argtable) {
 }
 
 void show_version(char *tool) {
-    printf("HPG Variant %s %s\nCopyright (C) 2013 Institute for Computational Medicine (CIPF).\n\
+    printf("HPG Variant %s %s\nCopyright (C) 2012-2013 Institute for Computational Medicine (CIPF).\n\
 This is free software; see the source for copying conditions.\n", tool, HPG_VARIANT_VERSION);
 }
 

src/hpg_variant_utils.h

@@ -35,7 +35,7 @@
 
 #include "shared_options.h"
 
-#define HPG_VARIANT_VERSION     "0.99.4"
+#define HPG_VARIANT_VERSION     "1.0"
 
 /* ***********************
  *     Initialization    *