Building scripts prepared for version RC1 (0.99.1)

Former-commit-id: 574673a

SConstruct

@@ -9,7 +9,7 @@ env = Environment(tools = ['default', 'packaging'],
                   CFLAGS = '-std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp',
                   CPPPATH = ['#', '#src', '#include', bioinfo_path, commons_path, math_path, '/usr/include', '/usr/local/include', '/usr/include/libxml2'],
                   LIBPATH = [commons_path, bioinfo_path, '/usr/lib', '/usr/local/lib'],
-                  LIBS = ['common', 'bioinfo', 'curl', 'gsl', 'gslcblas', 'm', 'xml2', 'z'],
+                  LIBS = ['common', 'bioinfo', 'curl', 'dl', 'gsl', 'gslcblas', 'm', 'xml2', 'z'],
                   LINKFLAGS = ['-fopenmp'])
 
 if int(ARGUMENTS.get('debug', '0')) == 1:
@@ -49,7 +49,7 @@ 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        = '0.5',
+                VERSION        = '0.99.1',
                 PACKAGEVERSION = 0,
                 PACKAGETYPE    = 'src_targz',
                 source         = env.FindSourceFiles() + env.FindHeaderFiles(progs) + 

deb/SConscript

@@ -4,10 +4,10 @@ Import('env') # exported by parent SConstruct
 
 # Here's the core info for the DEBIAN/control file of the package
 DEBNAME = "hpg-variant"
-DEBVERSION = "0.4"
+DEBVERSION = "0.99.1"
 DEBMAINT = "Cristina Yenyxe Gonzalez Garcia <[email protected]>"
 DEBARCH = "amd64"
-DEBDEPENDS = "libc6, libconfig8, libcurl4-openssl-dev, libgsl0ldbl, libxml2, zlib1g"
+DEBDEPENDS = "libc6, libcurl4-openssl-dev, libgsl0ldbl, libxml2, zlib1g"
 DEBSECTION = "science"
 DEBDESC = ''.join([ "Bioinformatics tool suite for analyzing genomic variations\n", 
 " HPG Variant is a suite for the analysis of genomic data extracted from Next\n",

rpm/SConscript

@@ -3,14 +3,14 @@ import hashlib, os, shutil, sys
 Import('env') # exported by parent SConstruct
 
 RPMNAME = "hpg-variant"
-RPMVERSION = "0.4"
+RPMVERSION = "0.99.1"
 RPMARCH = "x86_64"
-RPMBUILDREQUIRES = "gcc glibc-devel scons libconfig-devel libcurl-devel gsl-devel libxml2-devel zlib-devel".split(" ")
-RPMREQUIRES = "libconfig libcurl gsl libxml2 zlib".split(" ") # what are we dependent on?
+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"
 RPMDESC = "HPG Variant retrieves the effect of genome mutations and allows to conduct analysis"
 RPMSECTION = "Application/Engineering"
-RPMSOURCE = "hpg-variant-0.4.tar.gz"
+RPMSOURCE = "hpg-variant-0.99.1.tar.gz"
 RPMURL = "http://bioinfo.cipf.es"
 
 RPMBUILDIR = 'rpmbuild'

rpm/hpg-variant.spec

@@ -1,5 +1,5 @@
 %define name hpg-variant
-%define version 0.4
+%define version 0.99.1
 Name:           %{name}
 Version:        %{version}
 Release:        1%{?dist}
@@ -12,13 +12,12 @@ Source0:        %{name}-%{version}.tar.gz
 BuildRequires:  gcc
 BuildRequires:  glibc-devel
 BuildRequires:  scons
-BuildRequires:  libconfig-devel
 BuildRequires:  libcurl-devel
 BuildRequires:  gsl-devel
 BuildRequires:  libxml2-devel
+BuildRequires:  ncurses-devel
 BuildRequires:  zlib-devel
 
-Requires:       libconfig
 Requires:       libcurl
 Requires:       gsl
 Requires:       libxml2
@@ -55,6 +54,19 @@ cp bin/vcf-info-fields.conf %{buildroot}%{_sysconfdir}/%{name}/
 
 
 %changelog
+* Wed May 07 2013 Cristina Yenyxe Gonzalez <[email protected]> - 0.99.1
+- New VCF filters by gene, region+type, being or not an indel, and inheritance 
+  pattern (dominant/recessive)
+- Multi-threaded implementation of the VCF filtering tool
+- GFF/BED can be used as input for region filtering
+- New VCF statistics about mendelian errors per sample, being or not an indel, 
+  inheritance pattern per variant
+- Possibility of saving VCF statistics to SQLite DB file
+- Great reduction of memory usage, performance improvement upto 3x in VCF 
+  merging tool
+- VCF splitting by coverage intervals
+- Miscellaneous: Some library dependencies packaged inside the application
+
 * Mon Mar 04 2013 Cristina Yenyxe Gonzalez <[email protected]> - 0.4
 - Filter output uses default names, 'your_vcf_file.vcf.filtered' and
   'your_vcf_file.vcf.rejected', 'out' argument reserved for tool output