https://github.com/bcgsc/ntCard
Revision 86057528ebd297aa57c857bf4a03f691f0eb9425 authored by Étienne Mollier on 16 June 2021, 18:19:11 UTC, committed by Étienne Mollier on 16 June 2021, 18:19:11 UTC
Some differencies showed up in some of the tests. It turned out that some more overflows are occurring, but were not caught at build time. These adjustments allow the test suite to pass again. There are no changes of behavior on 64 bit platforms.
1 parent 5423687
Tip revision: 86057528ebd297aa57c857bf4a03f691f0eb9425 authored by Étienne Mollier on 16 June 2021, 18:19:11 UTC
fix test suite discrepancies on 32 bit
fix test suite discrepancies on 32 bit
Tip revision: 8605752
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
Computing file changes ...