Error msg on bad rules script

walaj · Apr 28, 2016 · 3091d64 · 3091d64
1 parent ae7a4bf
commit 3091d64
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Showing 8 changed files with 17 additions and 15 deletions.
diff --git a/Makefile.am b/Makefile.am
@@ -1,3 +1,3 @@
 AUTOMAKE_OPTIONS = foreign
 ##SUBDIRS = SnowTools/blat SnowTools/multifast-v1.4.2/ahocorasick SnowTools/SGA/Util SnowTools/SGA/SQG SnowTools/SGA/Bigraph SnowTools/SGA/Algorithm SnowTools/SGA/StringGraph SnowTools/SGA/SuffixTools SnowTools/bwa SnowTools/htslib SnowTools/src src
-SUBDIRS = SnowTools/blat SnowTools/multifast-v1.4.2/ahocorasick SnowTools/bwa SnowTools/htslib SnowTools/src src
+SUBDIRS = SnowTools/multifast-v1.4.2/ahocorasick SnowTools/htslib SnowTools/src src
diff --git a/Makefile.in b/Makefile.in
@@ -193,7 +193,7 @@ top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 AUTOMAKE_OPTIONS = foreign
-SUBDIRS = SnowTools/blat SnowTools/multifast-v1.4.2/ahocorasick SnowTools/bwa SnowTools/htslib SnowTools/src src
+SUBDIRS = SnowTools/multifast-v1.4.2/ahocorasick SnowTools/htslib SnowTools/src src
 all: config.h
 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
 

diff --git a/SnowTools b/SnowTools
diff --git a/configure b/configure
@@ -5124,7 +5124,7 @@ CFLAGS="$CFLAGS -O3"
 
 CPPFLAGS="$CPPFLAGS $boost_include"
 
-LDFLAGS="$LDFLAGS -L. $boost_lib_flag"
+LDFLAGS="$LDFLAGS $boost_lib_flag"
 
 LIBS="$LIBS -lpthread -lboost_regex"
 

diff --git a/configure.ac b/configure.ac
@@ -47,7 +47,7 @@ AC_SUBST(AM_CXXFLAGS, "-g -std=c++11 -Wall -Wextra $fail_on_warning -Wno-unknown
 AC_SUBST(CXXFLAGS, "$CXXFLAGS -O3")
 AC_SUBST(CFLAGS, "$CFLAGS -O3")
 AC_SUBST(CPPFLAGS, "$CPPFLAGS $boost_include")
-AC_SUBST(LDFLAGS, "$LDFLAGS -L. $boost_lib_flag")
+AC_SUBST(LDFLAGS, "$LDFLAGS $boost_lib_flag")
 AC_SUBST(LIBS, "$LIBS -lpthread -lboost_regex")
 
 # Make sure the bamtools headers can be found

diff --git a/src/Makefile.am b/src/Makefile.am
@@ -8,11 +8,10 @@ variant_CPPFLAGS = \
 
 variant_LDADD = \
 	$(top_builddir)/SnowTools/src/libsnowtools.a \
-	$(top_builddir)/SnowTools/bwa/libbwa.a \
 	$(top_builddir)/SnowTools/htslib/libhts.a \
 	$(top_builddir)/SnowTools/multifast-v1.4.2/ahocorasick/build/libahocorasick.a
 
 ##variant_LDFLAGS = -Wl,-Bstatic -lboost_regex
-##@boost_lib@/libboost_regex.a
+#variant_LDFLAGS = @boost_lib@/libboost_regex.a
 
 variant_SOURCES = variant.cpp VariantBamWalker.cpp
diff --git a/src/Makefile.in b/src/Makefile.in
@@ -49,7 +49,6 @@ am_variant_OBJECTS = variant-variant.$(OBJEXT) \
 	variant-VariantBamWalker.$(OBJEXT)
 variant_OBJECTS = $(am_variant_OBJECTS)
 variant_DEPENDENCIES = $(top_builddir)/SnowTools/src/libsnowtools.a \
-	$(top_builddir)/SnowTools/bwa/libbwa.a \
 	$(top_builddir)/SnowTools/htslib/libhts.a \
 	$(top_builddir)/SnowTools/multifast-v1.4.2/ahocorasick/build/libahocorasick.a
 DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
@@ -167,10 +166,11 @@ variant_CPPFLAGS = \
 
 variant_LDADD = \
 	$(top_builddir)/SnowTools/src/libsnowtools.a \
-	$(top_builddir)/SnowTools/bwa/libbwa.a \
 	$(top_builddir)/SnowTools/htslib/libhts.a \
 	$(top_builddir)/SnowTools/multifast-v1.4.2/ahocorasick/build/libahocorasick.a
 
+
+#variant_LDFLAGS = @boost_lib@/libboost_regex.a
 variant_SOURCES = variant.cpp VariantBamWalker.cpp
 all: all-am
 

diff --git a/src/VariantBamWalker.cpp b/src/VariantBamWalker.cpp
@@ -32,7 +32,7 @@ void VariantBamWalker::writeVariantBam()
       buffer_size = std::max((int32_t)r.Length() * 5, buffer_size);
 
       //std::cerr << "...r " << r << " rule " << rule << std::endl;
-      TrackSeenRead(r);
+      //TrackSeenRead(r);
 
       // add coverage
       if (max_cov != 0) {
@@ -138,15 +138,18 @@ void VariantBamWalker::TrackSeenRead(SnowTools::BamRead &r)
 void VariantBamWalker::printMessage(const SnowTools::BamRead &r) const 
 {
 
-  if (rc_main.total <= 0) {
-    std::cerr << "NO READS FOUND" << std::endl;
-    return;
-  }
-
   char buffer[90];
   std::string posstring = SnowTools::AddCommas<int>(r.Position());
   std::string chrname;
   try { chrname = SnowTools::GenomicRegion::chrToString(r.ChrID()); } catch(...) { chrname = "CHR_NAME_FAIL"; } 
+
+  if (rc_main.total <= 0) {
+    std::sprintf(buffer, "NO READS FOUND at %2s:%-11s",chrname.c_str(), posstring.c_str());
+    std::string outr(buffer);
+    std::cerr << outr << SnowTools::displayRuntime(start) << std::endl;
+    return;
+  }
+
   std::sprintf (buffer, "Read %11s at %2s:%-11s. Kept %10s (%2d%%) -- ",  
 		rc_main.totalString().c_str(), chrname.c_str(), posstring.c_str(),  
 		rc_main.keepString().c_str(), rc_main.percent());