1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
|
# ===========================================================================
#
# 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: std
std:
clean:
.PHONY: default std $(TARGETS)
PYTHON_VERS = $(shell python -V 2>&1)
# there is a separate set of sources for 2.5 and 2.6
ifeq (Python 2.6,$(shell expr "$(PYTHON_VERS)" : "\(Python 2.6\)"))
PYTHON_VERS=26
else
ifeq (Python 2.5,$(shell expr "$(PYTHON_VERS)" : "\(Python 2.5\)"))
PYTHON_VERS=26
else
PYTHON_VERS=
endif
endif
NGS_EXAMPLES = \
FragTest \
AlignTest \
AlignSliceTest \
PileupTest \
RefTest \
# ===========================================================================
#
# example runs
#
# NOTE: Expect libngs-sdk.so and libncbi-vdb.so somewhere inside $LD_LIBRARY_PATH
run_frag:
python FragTest$(PYTHON_VERS).py ERR225922 10000 2 $(REDIRECT)
run_align:
python AlignTest$(PYTHON_VERS).py ERR225922 10000 2 $(REDIRECT)
run_align_slice:
python AlignSliceTest$(PYTHON_VERS).py SRR1121656 1 1 9999 $(REDIRECT)
run_pileup:
python PileupTest$(PYTHON_VERS).py SRR1121656 1 9999 10003 $(REDIRECT)
run_ref:
python RefTest$(PYTHON_VERS).py SRR1121656 $(REDIRECT)
ALL_TESTS = run_frag run_align run_align_slice run_pileup run_ref
run_all: $(ALL_TESTS)
.PHONY: run_align run_align_slice run_frag
# ===========================================================================
#
# expected results for auto-testing
#
expected.txt update_expected:
if [ "$(PYTHON_VERS)" = "26" ] ; then \
echo Python 2.6 is not supported ; \
else \
rm -f expected.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>expected.txt" ; \
fi
run_and_diff: expected.txt
if [ "$(PYTHON_VERS)" = "26" ] ; then \
echo Python 2.6 is not supported ; \
else \
rm -f actual.txt; LD_LIBRARY_PATH=$(LD_LIBRARY_PATH) $(MAKE) run_all REDIRECT=">>actual.txt" ; \
diff expected.txt actual.txt && rm actual.txt && echo NGS Python examples work as expected ; \
fi
.PHONY: update_expected run_and_diff
|
