message: include htslib statically
diff: @@ -25,8 +25,8 @@ VCFLIB_ROOT=../vcflib
  TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
  HTSLIB_ROOT=$(TABIX_ROOT)/htslib
  -LIBS = -lseqlib -lhts -lz -lbz2 -lm -lpthread
  -INCLUDE = -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib -L$(SEQLIB_ROOT)/src -L$(SEQLIB_ROOT)/htslib
  +LIBS = -lseqlib -lz -lbz2 -llzma -lm -lpthread
  +INCLUDE = -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib -L$(SEQLIB_ROOT)/src
  #INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
  all: autoversion ../bin/freebayes ../bin/bamleftalign
  @@ -81,12 +81,12 @@ OBJECTS=BedReader.o \
  ../vcflib/smithwaterman/LeftAlign.o \
  ../vcflib/smithwaterman/Repeats.o \
  ../vcflib/smithwaterman/IndelAllele.o \
  - Variant.o
  + Variant.o \
  + $(SEQLIB_ROOT)/htslib/libhts.a
  seqlib=$(SEQLIB_ROOT)/src/libseqlib.a \
  $(SEQLIB_ROOT)/bwa/libbwa.a \
  - $(SEQLIB_ROOT)/fermi-lite/libfml.a \
  - $(SEQLIB_ROOT)/htslib/libhts.a
  + $(SEQLIB_ROOT)/fermi-lite/libfml.a
  HEADERS=multichoose.h version_git.h
  @@ -102,7 +102,7 @@ dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)
  $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
  bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o $(seqlib)
  - $(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o Fasta.o Utility.o LeftAlign.o IndelAllele.o split.o -o ../bin/bamleftalign $(LIBS)
  + $(CXX) $(CXXFLAGS) $(INCLUDE) $(OBJECTS) bamleftalign.o -o ../bin/bamleftalign $(LIBS)
  bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(SEQLIB_ROOT)/htslib/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS) $(seqlib)
  $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
  