From 450e934965f0f0f7ab7eb54dffc42e447fbbaae4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Salavert=20Torres?= Date: Fri, 20 Jun 2014 13:22:23 +0200 Subject: [PATCH 1/2] merge 24cd7e6 --- SConstruct | 2 +- lib/hpg-libs | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/SConstruct b/SConstruct index 62e015a..2bdbd01 100644 --- a/SConstruct +++ b/SConstruct @@ -14,7 +14,7 @@ compiler = ARGUMENTS.get('compiler', 'gcc') env = Environment(tools = ['default', 'packaging'], CC = compiler, variables = vars, - CFLAGS = '-std=c99 -D_XOPEN_SOURCE=600 -D_GNU_SOURCE -fopenmp -D_REENTRANT', + CFLAGS = '-Wall -std=c99 -D_XOPEN_SOURCE=700 -D_GNU_SOURCE -D_BSD_SOURCE -fopenmp -D_REENTRANT', CPPPATH = ['#', '#src', '#src/tools/bam', bioinfo_path, commons_path, "%s/commons/argtable" % commons_path, "%s/commons/config" % commons_path, system_include, '%s/libxml2' % system_include ], LIBPATH = [commons_path, bioinfo_path, system_libs], LIBS = ['xml2', 'm', 'z', 'curl', 'dl', 'bioinfo', 'common'], diff --git a/lib/hpg-libs b/lib/hpg-libs index af93f23..be1463a 160000 --- a/lib/hpg-libs +++ b/lib/hpg-libs @@ -1 +1 @@ -Subproject commit af93f2342f8260915576141c2dfeb97a5069f6c6 +Subproject commit be1463ab15464d2d39e8d5f365f369a51c333135 From 4acf0263ba5d066091272edcf230ccbc2f2c3d9b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jos=C3=A9=20Salavert=20Torres?= Date: Fri, 20 Jun 2014 14:14:21 +0200 Subject: [PATCH 2/2] Posible error in index builder function --- src/build-index/index_builder.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/build-index/index_builder.c b/src/build-index/index_builder.c index f1fb8e8..ed882c8 100644 --- a/src/build-index/index_builder.c +++ b/src/build-index/index_builder.c @@ -128,9 +128,9 @@ index_options_t *parse_index_options(int argc, char **argv) { if (strcmp(argv[0], "build-bwt-index") == 0) { mode = BWT_INDEX; + num_options += NUM_INDEX_BWT_OPTIONS; } else if (strcmp(argv[0], "build-sa-index") == 0) { mode = SA_INDEX; - num_options += NUM_INDEX_BWT_OPTIONS; } void **argtable = argtable_index_options_new(mode);//argtable_options_new(mode);