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https://github.com/bcgsc/ntCard
13 September 2022, 05:32:57 UTC
Revision 24d35c060840ab7389f3311c5bfd4a6a0a7c4b4c authored by Johnathan Wong on 23 January 2020, 17:22:40 UTC, committed by GitHub on 23 January 2020, 17:22:40 UTC 
use ntHash 2.1.0 (#36)
 
* The files in ntHash come from:
https://github.com/bcgsc/ntHash
Release 2.1.0
Downloaded using https://github.com/bcgsc/ntHash/archive/2.1.0.zip

* ntcard.cpp: use new ntHashIterator

* set up make distcheck CI

* azure: run make distcheck

* add Makefile needed for make distcheck

* Makefile.am: clean up downloaded files

* Makefile.am: add rm to code

* Makefile.am: use tabs

* Common: remove nthash.hpp

* Makefile.am: remove Common/nthash.hpp

* Common: remove ntHashIterator.hpp

* nthll.cpp: use vendored ntHashIterator.hpp

* Makefile.am: revert to previous ordering

* vendor/Makefile.am: add nthash.hpp
1 parent 8eb710f
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Tip revision: 24d35c060840ab7389f3311c5bfd4a6a0a7c4b4c authored by Johnathan Wong on 23 January 2020, 17:22:40 UTC
use ntHash 2.1.0 (#36)
Tip revision: 24d35c0
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

check-dna: test_k12.hist
	diff -q test_k12.hist $(srcdir)/data/test_k12.hist.good

check-rna: test-rna_k12.hist
	diff -q test-rna_k12.hist $(srcdir)/data/test_k12.hist.good

check: check-dna check-rna

# 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-rna-reads.fq.gz
	rm test-rna_k12.hist
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