Regarding running SingleSpilce.

requirements.md

get these with apt-get

• libfftw3-double3
• libfftw3-dev
• libboost-all-dev
• zlib1g-dev

...and don't install boost from sourceforge. It's quite big for a c library btw.

Feeling like your boost isn't located at /usr/include/boost? Consult whereis to find it out.

SingleSplice.diff

diff --git a/Makefile b/Makefile
index 5ac4ad6..4055a78 100644
--- a/Makefile
+++ b/Makefile
@@ -6,7 +6,7 @@
 #  2/13/16
 # ***********************************************************************
 SAMTOOLS=./diffsplice/src/parse_bam/samtools-0.1.18/
-BOOST=./boost_1_60_0/
+BOOST=/usr/include/boost
 .PHONY: clean
 
 all: test_ratio_change samtools parse_bam parse_frag diff_gtree diff_asm_analysis diff_expr_analysis diffsplice_exec
@@ -18,11 +18,11 @@ test_ratio_change.o: test_ratio_change.cc
 samtools: 
        ${MAKE} -C ${SAMTOOLS}
 parse_bam: diffsplice/src/parse_bam/parse_bam.cpp
-       g++ -I${SAMTOOLS} -g -O2 -Wall ./diffsplice/src/parse_bam/parse_bam.cpp -o ./diffsplice/bin/parse_bam -lz -L${SAMTOOLS} -lbam
+       g++ -I${SAMTOOLS} -g -O2 -Wall ./diffsplice/src/parse_bam/parse_bam.cpp -o ./diffsplice/bin/parse_bam -L${SAMTOOLS} -lbam -lz
 parse_frag: diffsplice/src/parse_frag/parse_frag.cpp
        g++ -m64 -o ./diffsplice/bin/parse_frag ./diffsplice/src/parse_frag/parse_frag.cpp
 diff_gtree: diffsplice/src/diff_gtree_ref/common_function.cpp diffsplice/src/diff_gtree_ref/decomposition.cpp diffsplice/src/diff_gtree_ref/estimation.cpp diffsplice/src/diff_gtree_ref/input_data.cpp diffsplice/src/diff_gtree_ref/output.cpp diffsplice/src/diff_gtree_ref/splice_graph.cpp diffsplice/src/diff_gtree_ref/cut_exon_bound.cpp diffsplice/src/diff_gtree_ref/wavelet2s.cpp diffsplice/src/diff_gtree_ref/main.cpp
-       g++ -m64 -I ./diffsplice/src/diff_gtree_ref/wavelet/include/ -o ./diffsplice/bin/diff_gtree diffsplice/src/diff_gtree_ref/common_function.cpp diffsplice/src/diff_gtree_ref/decomposition.cpp diffsplice/src/diff_gtree_ref/estimation.cpp diffsplice/src/diff_gtree_ref/input_data.cpp diffsplice/src/diff_gtree_ref/output.cpp diffsplice/src/diff_gtree_ref/splice_graph.cpp diffsplice/src/diff_gtree_ref/cut_exon_bound.cpp diffsplice/src/diff_gtree_ref/wavelet2s.cpp diffsplice/src/diff_gtree_ref/main.cpp -L diffsplice/src/diff_gtree_ref/wavelet/lib/ -lfftw3 -lm -std=c++0x 
+       g++ -m64 -I ./diffsplice/src/diff_gtree_ref/wavelet/include/ -o ./diffsplice/bin/diff_gtree diffsplice/src/diff_gtree_ref/common_function.cpp diffsplice/src/diff_gtree_ref/decomposition.cpp diffsplice/src/diff_gtree_ref/estimation.cpp diffsplice/src/diff_gtree_ref/input_data.cpp diffsplice/src/diff_gtree_ref/output.cpp diffsplice/src/diff_gtree_ref/splice_graph.cpp diffsplice/src/diff_gtree_ref/cut_exon_bound.cpp diffsplice/src/diff_gtree_ref/wavelet2s.cpp diffsplice/src/diff_gtree_ref/main.cpp -lfftw3 -lm -std=c++0x