diff --git a/src/Makefile.boilermake b/src/Makefile.boilermake index 353fa310..aaf37dd3 100644 --- a/src/Makefile.boilermake +++ b/src/Makefile.boilermake @@ -231,7 +231,7 @@ endef # COMPILE_C_CMDS - Commands for compiling C source code. define COMPILE_C_CMDS @mkdir -p $(dir $@) - $(strip ${CC} -o $@ -c -MD ${CFLAGS} ${SRC_CFLAGS} ${SRC_INCDIRS} ${EXT_INCDIRS} ${SRC_DEFS} $<) + $(strip ${CC} -o $@ -c -MD ${CFLAGS} ${SRC_CFLAGS} ${SRC_INCDIRS} ${SYS_INCDIRS} ${SRC_DEFS} $<) @cp ${@:%$(suffix $@)=%.d} ${@:%$(suffix $@)=%.P}; \ sed -e 's/#.*//' -e 's/^[^:]*: *//' -e 's/ *\\$$//' \ -e '/^$$/ d' -e 's/$$/ :/' < ${@:%$(suffix $@)=%.d} \ @@ -242,7 +242,7 @@ endef # COMPILE_CXX_CMDS - Commands for compiling C++ source code. define COMPILE_CXX_CMDS @mkdir -p $(dir $@) - $(strip ${CXX} -o $@ -c -MD ${CXXFLAGS} ${SRC_CXXFLAGS} ${SRC_INCDIRS} ${EXT_INCDIRS} ${SRC_DEFS} $<) + $(strip ${CXX} -o $@ -c -MD ${CXXFLAGS} ${SRC_CXXFLAGS} ${SRC_INCDIRS} ${SYS_INCDIRS} ${SRC_DEFS} $<) @cp ${@:%$(suffix $@)=%.d} ${@:%$(suffix $@)=%.P}; \ sed -e 's/#.*//' -e 's/^[^:]*: *//' -e 's/ *\\$$//' \ -e '/^$$/ d' -e 's/$$/ :/' < ${@:%$(suffix $@)=%.d} \ @@ -271,7 +271,7 @@ define INCLUDE_SUBMAKEFILE SRC_DEFS := SRC_INCDIRS := - EXT_INCDIRS := + SYS_INCDIRS := SUBMAKEFILES := @@ -330,8 +330,8 @@ define INCLUDE_SUBMAKEFILE SOURCES := $$(call CANONICAL_PATH,$${SOURCES}) SRC_INCDIRS := $$(call QUALIFY_PATH,$${DIR},$${SRC_INCDIRS}) SRC_INCDIRS := $$(call CANONICAL_PATH,$${SRC_INCDIRS}) - EXT_INCDIRS := $$(call QUALIFY_PATH,$${DIR},$${EXT_INCDIRS}) - EXT_INCDIRS := $$(call CANONICAL_PATH,$${EXT_INCDIRS}) + SYS_INCDIRS := $$(call QUALIFY_PATH,$${DIR},$${SYS_INCDIRS}) + SYS_INCDIRS := $$(call CANONICAL_PATH,$${SYS_INCDIRS}) # Save the list of source files for this target. $${TGT}_SOURCES += $${SOURCES} @@ -350,7 +350,7 @@ define INCLUDE_SUBMAKEFILE $${OBJS}: SRC_CXXFLAGS := $${SRC_CXXFLAGS} $${OBJS}: SRC_DEFS := $$(addprefix -D,$${SRC_DEFS}) $${OBJS}: SRC_INCDIRS := $$(addprefix -iquote,$${SRC_INCDIRS}) - $${OBJS}: EXT_INCDIRS := $$(addprefix -isystem,$${EXT_INCDIRS}) + $${OBJS}: SYS_INCDIRS := $$(addprefix -isystem,$${SYS_INCDIRS}) endif ifneq "$$(strip $${SUBMAKEFILES})" "" diff --git a/src/canu b/src/canu index 6b86fef7..bae64262 160000 --- a/src/canu +++ b/src/canu @@ -1 +1 @@ -Subproject commit 6b86fef7a7862f75d1d0d7cdcf229ae0e9d0c93e +Subproject commit bae6426223a5542d23da245fda57286da7c3ef4b diff --git a/src/main.mk b/src/main.mk index b6e9250a..bcb5fc80 100644 --- a/src/main.mk +++ b/src/main.mk @@ -47,37 +47,29 @@ SOURCES := ${CANUROOT}utility/src/align/align-ksw2-driver.C \ ${CANUROOT}utility/src/kmers-v1/kmers-exact.C \ ${CANUROOT}utility/src/kmers-v1/kmers-files.C \ ${CANUROOT}utility/src/kmers-v1/kmers-histogram.C \ + ${CANUROOT}utility/src/kmers-v1/kmers-histogram-ploidy.C \ ${CANUROOT}utility/src/kmers-v1/kmers-reader.C \ ${CANUROOT}utility/src/kmers-v1/kmers-writer-block.C \ ${CANUROOT}utility/src/kmers-v1/kmers-writer-stream.C \ ${CANUROOT}utility/src/kmers-v1/kmers-writer.C \ ${CANUROOT}utility/src/kmers-v1/kmers.C \ \ - ${CANUROOT}utility/src/kmers-v2/kmers-exact.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-files.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-histogram.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-reader-dump.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-reader.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-writer-block.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-writer-stream.C \ - ${CANUROOT}utility/src/kmers-v2/kmers-writer.C \ - ${CANUROOT}utility/src/kmers-v2/kmers.C \ - \ ${CANUROOT}utility/src/math/md5-v1.C \ ${CANUROOT}utility/src/math/mt19937ar-v1.C \ ${CANUROOT}utility/src/math/sampledDistribution-v1.C \ \ ${CANUROOT}utility/src/parasail/cpuid.c \ + ${CANUROOT}utility/src/parasail/cigar.c \ ${CANUROOT}utility/src/parasail/memory.c \ ${CANUROOT}utility/src/parasail/sg.c \ ${CANUROOT}utility/src/parasail/sg_trace.c \ - ${CANUROOT}utility/src/parasail/sg_qx_dispatch.c \ ${CANUROOT}utility/src/parasail/sg_qb_de_dispatch.c \ ${CANUROOT}utility/src/parasail/sg_qe_db_dispatch.c \ - ${CANUROOT}utility/src/parasail/cigar.c \ + ${CANUROOT}utility/src/parasail/sg_qx_dispatch.c \ \ ${CANUROOT}utility/src/sequence/dnaSeq-v1.C \ - ${CANUROOT}utility/src/sequence/dnaSeqFile-v1.C \ + ${CANUROOT}utility/src/sequence/bufSeqFile-v1.C \ + ${CANUROOT}utility/src/sequence/htsSeqFile-v1.C \ ${CANUROOT}utility/src/sequence/sequence-v1.C \ \ ${CANUROOT}utility/src/system/logging-v1.C \ @@ -120,6 +112,55 @@ SOURCES := ${CANUROOT}utility/src/align/align-ksw2-driver.C \ ${CANUROOT}gfa/gfa.C \ ${CANUROOT}gfa/bed.C +SOURCES += ${CANUROOT}utility/src/htslib/hts/bcf_sr_sort.c \ + ${CANUROOT}utility/src/htslib/hts/bgzf.c \ + ${CANUROOT}utility/src/htslib/hts/errmod.c \ + ${CANUROOT}utility/src/htslib/hts/faidx.c \ + ${CANUROOT}utility/src/htslib/hts/header.c \ + ${CANUROOT}utility/src/htslib/hts/hfile.c \ + ${CANUROOT}utility/src/htslib/hts/hfile_libcurl.c \ + ${CANUROOT}utility/src/htslib/hts/hfile_s3.c \ + ${CANUROOT}utility/src/htslib/hts/hts.c \ + ${CANUROOT}utility/src/htslib/hts/hts_expr.c \ + ${CANUROOT}utility/src/htslib/hts/hts_os.c \ + ${CANUROOT}utility/src/htslib/hts/kfunc.c \ + ${CANUROOT}utility/src/htslib/hts/kstring.c \ + ${CANUROOT}utility/src/htslib/hts/md5.c \ + ${CANUROOT}utility/src/htslib/hts/multipart.c \ + ${CANUROOT}utility/src/htslib/hts/probaln.c \ + ${CANUROOT}utility/src/htslib/hts/realn.c \ + ${CANUROOT}utility/src/htslib/hts/regidx.c \ + ${CANUROOT}utility/src/htslib/hts/region.c \ + ${CANUROOT}utility/src/htslib/hts/sam.c \ + ${CANUROOT}utility/src/htslib/hts/synced_bcf_reader.c \ + ${CANUROOT}utility/src/htslib/hts/tbx.c \ + ${CANUROOT}utility/src/htslib/hts/textutils.c \ + ${CANUROOT}utility/src/htslib/hts/thread_pool.c \ + ${CANUROOT}utility/src/htslib/hts/vcf.c \ + ${CANUROOT}utility/src/htslib/hts/vcf_sweep.c \ + ${CANUROOT}utility/src/htslib/hts/vcfutils.c \ + ${CANUROOT}utility/src/htslib/cram/cram_codecs.c \ + ${CANUROOT}utility/src/htslib/cram/cram_decode.c \ + ${CANUROOT}utility/src/htslib/cram/cram_encode.c \ + ${CANUROOT}utility/src/htslib/cram/cram_external.c \ + ${CANUROOT}utility/src/htslib/cram/cram_index.c \ + ${CANUROOT}utility/src/htslib/cram/cram_io.c \ + ${CANUROOT}utility/src/htslib/cram/cram_stats.c \ + ${CANUROOT}utility/src/htslib/cram/mFILE.c \ + ${CANUROOT}utility/src/htslib/cram/open_trace_file.c \ + ${CANUROOT}utility/src/htslib/cram/pooled_alloc.c \ + ${CANUROOT}utility/src/htslib/cram/string_alloc.c \ + ${CANUROOT}utility/src/htslib/htscodecs/arith_dynamic.c \ + ${CANUROOT}utility/src/htslib/htscodecs/fqzcomp_qual.c \ + ${CANUROOT}utility/src/htslib/htscodecs/htscodecs.c \ + ${CANUROOT}utility/src/htslib/htscodecs/pack.c \ + ${CANUROOT}utility/src/htslib/htscodecs/rANS_static.c \ + ${CANUROOT}utility/src/htslib/htscodecs/rANS_static32x16pr.c \ + ${CANUROOT}utility/src/htslib/htscodecs/rANS_static32x16pr_neon.c \ + ${CANUROOT}utility/src/htslib/htscodecs/rANS_static4x16pr.c \ + ${CANUROOT}utility/src/htslib/htscodecs/rle.c \ + ${CANUROOT}utility/src/htslib/htscodecs/tokenise_name3.c \ + ${CANUROOT}utility/src/htslib/htscodecs/utils.c ifeq (${BUILDSTACKTRACE}, 1) SOURCES += ${CANUROOT}utility/src/system/libbacktrace/atomic.c \ @@ -148,6 +189,10 @@ SRC_INCDIRS := . \ ${CANUROOT}utgcns/libpbutgcns \ ${CANUROOT}overlapBasedTrimming \ +SYS_INCDIRS += $(shell pkg-config --cflags-only-I openssl libcurl liblzma | sed s:-I/:/:g) +LDFLAGS += $(shell pkg-config --libs-only-L openssl libcurl liblzma) +LDLIBS += $(shell pkg-config --libs-only-l openssl libcurl liblzma) -lz -lbz2 + SUBMAKEFILES := ${CANUROOT}stores/ovStoreBuild.mk \ ${CANUROOT}stores/ovStoreConfig.mk \ ${CANUROOT}stores/ovStoreBucketizer.mk \