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# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
default: runtests
TOP ?= $(abspath ../..)
MODULE = test/sra-pileup
TEST_TOOLS =
include $(TOP)/build/Makefile.env
CONFIGTOUSE ?= NCBI_SETTINGS
DIRTOTEST ?= $(BINDIR)
$(TEST_TOOLS): makedirs
@ $(MAKE_CMD) $(TEST_BINDIR)/$@
ifdef PYTHON
runtests: announce check_exit_code # check_skiplist
slowtests: announce fastq_dump_vs_sam_dump sam_dump_spotgroup_for_all
else
runtests: ;
slowtests: ;
endif
announce:
@echo Testing $(DIRTOTEST) CONFIGTOUSE=$(CONFIGTOUSE)
#-------------------------------------------------------------------------------
# scripted tests
#
check_exit_code:
@ $(CONFIGTOUSE)=/ $(PYTHON) \
$(TOP)/build/check-exit-code.py $(DIRTOTEST)/sra-pileup
check_skiplist:
@ $(CONFIGTOUSE)=/ $(PYTHON) check_skiplist.py $(DIRTOTEST)/sra-pileup
ACC = SRR3332402
#-------------------------------------------------------------------------------
# testing if sam-dump and fastq-dump produce the same READ/QUALITY values
#
fastq_dump_vs_sam_dump :
@ $(CONFIGTOUSE)=/ $(PYTHON) test_diff_fastq_dump_vs_sam_dump.py \
-a $(ACC) -f $(DIRTOTEST)/fastq-dump -m $(DIRTOTEST)/sam-dump
#-------------------------------------------------------------------------------
# testing if sam-dump and fastq-dump produce the same READ/QUALITY values
#
sam_dump_spotgroup_for_all :
@ $(CONFIGTOUSE)=/ $(PYTHON) test_all_sam_dump_has_spotgroup.py \
-a $(ACC) -m $(DIRTOTEST)/sam-dump
.PHONY: $(TEST_TOOLS)
clean: stdclean
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