changed to open interval merge in merge overlapping

Author: Jeremiah Wala

SeqLib/GenomicRegionCollection.cpp

@@ -343,7 +343,7 @@ void GenomicRegionCollection<T>::MergeOverlappingIntervals() {
   typename std::list<T>::iterator inext(intervals.begin());
   ++inext;
   for (typename std::list<T>::iterator i(intervals.begin()), iend(intervals.end()); inext != iend;) {
-    if((i->pos2 > inext->pos1) && (i->chr == inext->chr))
+    if((i->pos2 >= inext->pos1) && (i->chr == inext->chr)) // change >= to > to not overlap touching intervals (eg [4,5][5,6])
       {
 	if(i->pos2 >= inext->pos2) intervals.erase(inext++);
 	else if(i->pos2 < inext->pos2)

SeqLib/GenomicRegionCollection.h

@@ -115,6 +115,7 @@ class GenomicRegionCollection {
   void CreateTreeMap();
 
   /** Reduces the GenomicRegion objects to minimal set by merging overlapping intervals
+   * @note This will merge intervals that touch. eg [4,6] and [6,8]
    * @note This will also call CreateTreeMap() at end to re-create the interval tree
    */
   void MergeOverlappingIntervals();

fermi-lite

@@ -39,7 +39,6 @@ am__aclocal_m4_deps = $(top_srcdir)/configure.ac
 am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 	$(ACLOCAL_M4)
 mkinstalldirs = $(install_sh) -d
-CONFIG_HEADER = $(top_builddir)/config.h
 CONFIG_CLEAN_FILES =
 CONFIG_CLEAN_VPATH_FILES =
 LIBRARIES = $(noinst_LIBRARIES)
@@ -60,7 +59,7 @@ am_libseqlib_a_OBJECTS = libseqlib_a-FastqReader.$(OBJEXT) \
 	libseqlib_a-FermiAssembler.$(OBJEXT) \
 	libseqlib_a-BamHeader.$(OBJEXT)
 libseqlib_a_OBJECTS = $(am_libseqlib_a_OBJECTS)
-DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir)
+DEFAULT_INCLUDES = -I.@am__isrc@
 depcomp = $(SHELL) $(top_srcdir)/depcomp
 am__depfiles_maybe = depfiles
 am__mv = mv -f
@@ -139,6 +138,7 @@ am__quote = @am__quote@
 am__tar = @am__tar@
 am__untar = @am__untar@
 bindir = @bindir@
+boost_lib = @boost_lib@
 build_alias = @build_alias@
 builddir = @builddir@
 datadir = @datadir@