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Enable canu bamoutput branch. Update Makefile to agree with latest, a…
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…dd htslib, etc.
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@brianwalenz
brianwalenz committed Jul 7, 2024
1 parent 3538dcc commit 97ed6bd
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Showing 3 changed files with 65 additions and 20 deletions.
12 changes: 6 additions & 6 deletions src/Makefile.boilermake
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Original file line number Diff line number Diff line change
Expand Up @@ -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} \
Expand All @@ -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} \
Expand Down Expand Up @@ -271,7 +271,7 @@ define INCLUDE_SUBMAKEFILE
SRC_DEFS :=
SRC_INCDIRS :=

EXT_INCDIRS :=
SYS_INCDIRS :=

SUBMAKEFILES :=

Expand Down Expand Up @@ -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}
Expand All @@ -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})" ""
Expand Down
2 changes: 1 addition & 1 deletion src/canu
Submodule canu updated 30 files
+30 −2 README.md
+36 −0 scripts/build-all-compilers.sh
+3 −3 src/Makefile
+6 −6 src/Makefile.boilermake
+1 −1 src/gfa/alignGFA.C
+1 −1 src/haplotyping/splitHaplotype.C
+57 −11 src/main.mk
+1 −1 src/meryl
+16 −1 src/overlapErrorAdjustment/findErrors-Output.C
+4 −4 src/overlapInCore/edalign.C
+2 −1 src/pipelines/canu.pl
+56 −13 src/pipelines/canu/Consensus.pm
+44 −1 src/pipelines/canu/Defaults.pm
+5 −3 src/pipelines/canu/HaplotypeReads.pm
+1 −1 src/seqrequester
+6 −1 src/stores/sqCache.C
+1 −1 src/stores/sqStoreCreate.C
+179 −33 src/stores/tgTig.C
+22 −12 src/stores/tgTig.H
+14 −13 src/utgcns/layoutToPackage.C
+35 −3 src/utgcns/libpbutgcns/AlnGraphBoost.C
+10 −4 src/utgcns/libpbutgcns/AlnGraphBoost.H
+397 −489 src/utgcns/unitigConsensus.C
+49 −50 src/utgcns/unitigConsensus.H
+8 −6 src/utgcns/utgcns-parameters.C
+31 −46 src/utgcns/utgcns-processTigs.C
+61 −2 src/utgcns/utgcns.C
+12 −0 src/utgcns/utgcns.H
+4 −1 src/utgcns/utgcns.mk
+1 −1 src/utility
71 changes: 58 additions & 13 deletions src/main.mk
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 \
Expand Down Expand Up @@ -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 \
Expand Down Expand Up @@ -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 \
Expand Down

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