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Jeremiah Wala
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made non-api folder
1 parent e73ddbd commit f5da9c9

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-254
lines changed

‎.travis.scripts/coveralls.sh

+1-1
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@@ -20,7 +20,7 @@ echo "...running unit tests and code coverage"
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make
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./seq_test
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23-
EXCL="-e seq_test/seq_test.cpp -e htslib -e bwa -e fermi-lite -e config.h -e seq_test/config.h -e seq_test/config.h -e src/jsoncpp.cpp -e src/json"
23+
EXCL="-e src/non_api -e seq_test/seq_test.cpp -e htslib -e bwa -e fermi-lite -e config.h -e seq_test/config.h -e seq_test/config.h -e src/jsoncpp.cpp -e src/json"
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cpp-coveralls -r ../ -t ${COVERALLS_TOKEN} ${EXCL} ##--dryrun
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#find ./ -type f -regex ".*/[a-z_]+.*gcov" -delete
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#cpp-coveralls -r ../ -t ${COVERALLS_TOKEN} ${EXCL} -n

‎src/issue_tracking.md ‎issue_tracking.md

File renamed without changes.

‎seq_test/Makefile.am

+3-3
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@@ -16,8 +16,8 @@ seq_test_LDFLAGS = --coverage
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seq_test_SOURCES = seq_test.cpp \
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../src/GenomicRegion.cpp \
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../src/Histogram.cpp ../src/BamWriter.cpp ../src/BamReader.cpp ../src/BamStats.cpp \
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../src/BamWriter.cpp ../src/BamReader.cpp \
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../src/ReadFilter.cpp ../src/SeqLibUtils.cpp ../src/BamRecord.cpp \
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../src/BWAWrapper.cpp ../src/STCoverage.cpp \
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../src/Fractions.cpp ../src/RefGenome.cpp ../src/SeqPlot.cpp ../src/BamHeader.cpp \
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../src/BWAWrapper.cpp \
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../src/RefGenome.cpp ../src/SeqPlot.cpp ../src/BamHeader.cpp \
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../src/FermiAssembler.cpp ../src/ssw_cpp.cpp ../src/ssw.c ../src/jsoncpp.cpp

‎seq_test/Makefile.in

+6-68
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@@ -51,12 +51,10 @@ CONFIG_CLEAN_VPATH_FILES =
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am__installdirs = "$(DESTDIR)$(bindir)"
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PROGRAMS = $(bin_PROGRAMS)
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am_seq_test_OBJECTS = seq_test-seq_test.$(OBJEXT) \
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seq_test-GenomicRegion.$(OBJEXT) seq_test-Histogram.$(OBJEXT) \
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seq_test-BamWriter.$(OBJEXT) seq_test-BamReader.$(OBJEXT) \
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seq_test-BamStats.$(OBJEXT) seq_test-ReadFilter.$(OBJEXT) \
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seq_test-GenomicRegion.$(OBJEXT) seq_test-BamWriter.$(OBJEXT) \
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seq_test-BamReader.$(OBJEXT) seq_test-ReadFilter.$(OBJEXT) \
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seq_test-SeqLibUtils.$(OBJEXT) seq_test-BamRecord.$(OBJEXT) \
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seq_test-BWAWrapper.$(OBJEXT) seq_test-STCoverage.$(OBJEXT) \
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seq_test-Fractions.$(OBJEXT) seq_test-RefGenome.$(OBJEXT) \
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seq_test-BWAWrapper.$(OBJEXT) seq_test-RefGenome.$(OBJEXT) \
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seq_test-SeqPlot.$(OBJEXT) seq_test-BamHeader.$(OBJEXT) \
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seq_test-FermiAssembler.$(OBJEXT) seq_test-ssw_cpp.$(OBJEXT) \
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seq_test-ssw.$(OBJEXT) seq_test-jsoncpp.$(OBJEXT)
@@ -201,10 +199,10 @@ seq_test_LDADD = \
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seq_test_LDFLAGS = --coverage
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seq_test_SOURCES = seq_test.cpp \
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../src/GenomicRegion.cpp \
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../src/Histogram.cpp ../src/BamWriter.cpp ../src/BamReader.cpp ../src/BamStats.cpp \
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../src/BamWriter.cpp ../src/BamReader.cpp \
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../src/ReadFilter.cpp ../src/SeqLibUtils.cpp ../src/BamRecord.cpp \
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../src/BWAWrapper.cpp ../src/STCoverage.cpp \
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../src/Fractions.cpp ../src/RefGenome.cpp ../src/SeqPlot.cpp ../src/BamHeader.cpp \
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../src/BWAWrapper.cpp \
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../src/RefGenome.cpp ../src/SeqPlot.cpp ../src/BamHeader.cpp \
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../src/FermiAssembler.cpp ../src/ssw_cpp.cpp ../src/ssw.c ../src/jsoncpp.cpp
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all: config.h
@@ -314,15 +312,11 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-BamHeader.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-BamReader.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-BamRecord.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-BamStats.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-BamWriter.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-FermiAssembler.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-Fractions.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-GenomicRegion.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-Histogram.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-ReadFilter.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-RefGenome.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-STCoverage.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-SeqLibUtils.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-SeqPlot.Po@am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/seq_test-jsoncpp.Po@am__quote@
@@ -400,20 +394,6 @@ seq_test-GenomicRegion.obj: ../src/GenomicRegion.cpp
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-GenomicRegion.obj `if test -f '../src/GenomicRegion.cpp'; then $(CYGPATH_W) '../src/GenomicRegion.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/GenomicRegion.cpp'; fi`
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seq_test-Histogram.o: ../src/Histogram.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-Histogram.o -MD -MP -MF $(DEPDIR)/seq_test-Histogram.Tpo -c -o seq_test-Histogram.o `test -f '../src/Histogram.cpp' || echo '$(srcdir)/'`../src/Histogram.cpp
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@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/seq_test-Histogram.Tpo $(DEPDIR)/seq_test-Histogram.Po
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='../src/Histogram.cpp' object='seq_test-Histogram.o' libtool=no @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-Histogram.o `test -f '../src/Histogram.cpp' || echo '$(srcdir)/'`../src/Histogram.cpp
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seq_test-Histogram.obj: ../src/Histogram.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-Histogram.obj -MD -MP -MF $(DEPDIR)/seq_test-Histogram.Tpo -c -o seq_test-Histogram.obj `if test -f '../src/Histogram.cpp'; then $(CYGPATH_W) '../src/Histogram.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/Histogram.cpp'; fi`
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@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/seq_test-Histogram.Tpo $(DEPDIR)/seq_test-Histogram.Po
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='../src/Histogram.cpp' object='seq_test-Histogram.obj' libtool=no @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-Histogram.obj `if test -f '../src/Histogram.cpp'; then $(CYGPATH_W) '../src/Histogram.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/Histogram.cpp'; fi`
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seq_test-BamWriter.o: ../src/BamWriter.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-BamWriter.o -MD -MP -MF $(DEPDIR)/seq_test-BamWriter.Tpo -c -o seq_test-BamWriter.o `test -f '../src/BamWriter.cpp' || echo '$(srcdir)/'`../src/BamWriter.cpp
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@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/seq_test-BamWriter.Tpo $(DEPDIR)/seq_test-BamWriter.Po
@@ -442,20 +422,6 @@ seq_test-BamReader.obj: ../src/BamReader.cpp
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-BamReader.obj `if test -f '../src/BamReader.cpp'; then $(CYGPATH_W) '../src/BamReader.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/BamReader.cpp'; fi`
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seq_test-BamStats.o: ../src/BamStats.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-BamStats.o -MD -MP -MF $(DEPDIR)/seq_test-BamStats.Tpo -c -o seq_test-BamStats.o `test -f '../src/BamStats.cpp' || echo '$(srcdir)/'`../src/BamStats.cpp
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@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/seq_test-BamStats.Tpo $(DEPDIR)/seq_test-BamStats.Po
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-BamStats.o `test -f '../src/BamStats.cpp' || echo '$(srcdir)/'`../src/BamStats.cpp
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seq_test-BamStats.obj: ../src/BamStats.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-BamStats.obj -MD -MP -MF $(DEPDIR)/seq_test-BamStats.Tpo -c -o seq_test-BamStats.obj `if test -f '../src/BamStats.cpp'; then $(CYGPATH_W) '../src/BamStats.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/BamStats.cpp'; fi`
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@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/seq_test-BamStats.Tpo $(DEPDIR)/seq_test-BamStats.Po
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ source='../src/BamStats.cpp' object='seq_test-BamStats.obj' libtool=no @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCXX_FALSE@ DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-BamStats.obj `if test -f '../src/BamStats.cpp'; then $(CYGPATH_W) '../src/BamStats.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/BamStats.cpp'; fi`
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seq_test-ReadFilter.o: ../src/ReadFilter.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-ReadFilter.o -MD -MP -MF $(DEPDIR)/seq_test-ReadFilter.Tpo -c -o seq_test-ReadFilter.o `test -f '../src/ReadFilter.cpp' || echo '$(srcdir)/'`../src/ReadFilter.cpp
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@am__fastdepCXX_TRUE@ $(am__mv) $(DEPDIR)/seq_test-ReadFilter.Tpo $(DEPDIR)/seq_test-ReadFilter.Po
@@ -512,34 +478,6 @@ seq_test-BWAWrapper.obj: ../src/BWAWrapper.cpp
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-BWAWrapper.obj `if test -f '../src/BWAWrapper.cpp'; then $(CYGPATH_W) '../src/BWAWrapper.cpp'; else $(CYGPATH_W) '$(srcdir)/../src/BWAWrapper.cpp'; fi`
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seq_test-STCoverage.o: ../src/STCoverage.cpp
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@am__fastdepCXX_TRUE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -MT seq_test-STCoverage.o -MD -MP -MF $(DEPDIR)/seq_test-STCoverage.Tpo -c -o seq_test-STCoverage.o `test -f '../src/STCoverage.cpp' || echo '$(srcdir)/'`../src/STCoverage.cpp
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@am__fastdepCXX_FALSE@ $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(seq_test_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -c -o seq_test-Fractions.o `test -f '../src/Fractions.cpp' || echo '$(srcdir)/'`../src/Fractions.cpp
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‎seq_test/seq_test.cpp

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@@ -790,4 +790,3 @@ BOOST_AUTO_TEST_CASE( sequtils ) {
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‎src/Makefile.am

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noinst_LIBRARIES = libseqlib.a
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libseqlib_a_CPPFLAGS = \
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-I.. \
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libseqlib_a_SOURCES = ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
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GenomicRegion.cpp Histogram.cpp RefGenome.cpp \
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BamWriter.cpp BamReader.cpp BamStats.cpp SeqLibUtils.cpp \
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BWAWrapper.cpp BamRecord.cpp \
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STCoverage.cpp Fractions.cpp FermiAssembler.cpp \
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BamHeader.cpp
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GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp SeqLibUtils.cpp \
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BWAWrapper.cpp BamRecord.cpp FermiAssembler.cpp BamHeader.cpp

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