https://github.com/bcgsc/ntCard
Tip revision: 741c9417282570a71c4042f0d2022493f26c4e49 authored by Johnathan Wong on 27 January 2020, 22:56:49 UTC
release 1.2.1 (#40)
release 1.2.1 (#40)
Tip revision: 741c941
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-reads.fa: test-reads.fq.gz
zcat test-reads.fq.gz |sed -n '1~4s/^@/>/p;2~4p' > test-reads.fa
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-fa_k12.hist: test-reads.fa
./ntcard -k 12 -p test-fa test-reads.fa
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
test-fa-gap_k12.hist: test-reads.fa
./ntcard -k 12 -p test-fa-gap -g 2 test-reads.fa
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-fa: test-fa_k12.hist
diff -q test-fa_k12.hist $(srcdir)/data/test_k12.hist.good
check-fa-gap: test-fa-gap_k12.hist
diff -q test-fa-gap_k12.hist $(srcdir)/data/test-gap_k12.hist.good
check: check-dna check-rna check-fa check-dna-gap check-rna-gap check-fa-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
rm test-reads.fa
rm test-fa_k12.hist
rm test-fa-gap_k12.hist