Revision e2eafd5390491614a5b8a9fa4fca97e72ac97a2e authored by Johnathan Wong on 24 January 2020, 22:42:01 UTC, committed by GitHub on 24 January 2020, 22:42:01 UTC
* add gap seed estimation * nthash.hpp: revert changes to table * ntcard.hpp: fix format * ntcard.hpp: remove comment * ntcard.hpp: break when multiple is specified with -g * ntcard.cpp: gap seed for fa and sam * ntcard: update headers * ntcard: clang-formatted * vendor: undo changes * Common: remove stHashIterator * configure.ac: revert * vendor/Makefile.am: add stHashIterator.hpp * Makefile.am: remove m4 * vendor: undo changes * ntcard: c++03 compliant * clang-format: c++03 compliant * clang-format: correct syntax * clang-format: capitalization * ntcard: remove empty line * add gap seed test
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Makefile.am
bin_PROGRAMS = ntcard nthll
ntcard_CPPFLAGS = -I$(top_srcdir)/Common
ntcard_SOURCES = \
Common/Uncompress.cpp \
Common/Uncompress.h \
Common/SignalHandler.cpp \
Common/SignalHandler.h \
Common/StringUtil.h \
Common/Fcontrol.cpp \
Common/Fcontrol.h \
ntcard.cpp
nthll_CPPFLAGS = -I$(top_srcdir)/Common
nthll_SOURCES = \
Common/Uncompress.cpp \
Common/Uncompress.h \
Common/SignalHandler.cpp \
Common/SignalHandler.h \
Common/Fcontrol.cpp \
Common/Fcontrol.h \
nthll.cpp
dist_doc_DATA = \
ChangeLog \
CITATION.bib \
LICENSE \
README.md
EXTRA_DIST= autogen.sh
SUBDIRS = \
vendor \
data
test-reads.fq.gz:
wget https://www.bcgsc.ca/downloads/btl/ntcard/test-reads.fq.gz
test-rna-reads.fq.gz:
wget https://www.bcgsc.ca/downloads/btl/ntcard/test-rna-reads.fq.gz
test_k12.hist: test-reads.fq.gz
./ntcard -k 12 -p test test-reads.fq.gz
test-rna_k12.hist: test-rna-reads.fq.gz
./ntcard -k 12 -p test-rna test-rna-reads.fq.gz
test-gap_k12.hist: test-reads.fq.gz
./ntcard -k 12 -p test-gap -g 2 test-reads.fq.gz
test-rna-gap_k12.hist: test-rna-reads.fq.gz
./ntcard -k 12 -p test-rna-gap -g 2 test-rna-reads.fq.gz
check-dna: test_k12.hist
diff -q test_k12.hist $(srcdir)/data/test_k12.hist.good
check-dna-gap: test-gap_k12.hist
diff -q test-gap_k12.hist $(srcdir)/data/test-gap_k12.hist.good
check-rna: test-rna_k12.hist
diff -q test-rna_k12.hist $(srcdir)/data/test_k12.hist.good
check-rna-gap: test-rna-gap_k12.hist
diff -q test-rna-gap_k12.hist $(srcdir)/data/test-gap_k12.hist.good
check: check-dna check-rna check-dna-gap check-rna-gap
# Check the C++ source code for white-space errors with clang-format.
clang-format:
for i in ntcard.cpp; do clang-format -style=file $$i >$$i.fixed; done
for i in ntcard.cpp; do diff -su $$i $$i.fixed && rm -f $$i.fixed; done
if ls *.fixed; then exit 1; fi
clean-local:
rm test-reads.fq.gz
rm test_k12.hist
rm test-gap_k12.hist
rm test-rna-reads.fq.gz
rm test-rna_k12.hist
rm test-rna-gap_k12.hist
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