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/dports/biology/stacks/stacks-2.4/htslib/
H A DMakefile.am13 cram/cram.h \
14 cram/cram_codecs.c \
15 cram/cram_codecs.h \
23 cram/cram_io.c \
24 cram/cram_io.h \
30 cram/files.c \
31 cram/mFILE.c \
32 cram/mFILE.h \
33 cram/misc.h \
36 cram/os.h \
[all …]
H A DMakefile.in105 cram/cram_stats.$(OBJEXT) cram/files.$(OBJEXT) \
282 cram/cram.h \
416 cram/cram_codecs.$(OBJEXT): cram/$(am__dirstamp) \
418 cram/cram_decode.$(OBJEXT): cram/$(am__dirstamp) \
420 cram/cram_encode.$(OBJEXT): cram/$(am__dirstamp) \
424 cram/cram_index.$(OBJEXT): cram/$(am__dirstamp) \
426 cram/cram_io.$(OBJEXT): cram/$(am__dirstamp) \
430 cram/cram_stats.$(OBJEXT): cram/$(am__dirstamp) \
432 cram/files.$(OBJEXT): cram/$(am__dirstamp) \
434 cram/mFILE.$(OBJEXT): cram/$(am__dirstamp) \
[all …]
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/
H A Dhtslib.mk51 $(HTSDIR)/htslib/cram.h \
109 $(HTSDIR)/cram/cram.h \
126 $(HTSDIR)/cram/files.c \
127 $(HTSDIR)/cram/mFILE.c \
128 $(HTSDIR)/cram/mFILE.h \
129 $(HTSDIR)/cram/misc.h \
132 $(HTSDIR)/cram/os.h \
142 $(HTSDIR)/cram/vlen.c \
143 $(HTSDIR)/cram/vlen.h \
144 $(HTSDIR)/cram/zfio.c \
[all …]
H A DMakefile185 …cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encod…
319 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
326 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
327 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
328 cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(cram_os_h) cram/mFILE.h cram/vlen.h
330 cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram…
331 cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_…
332 cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string…
333 cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
335 cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h $(cram_os_h)
[all …]
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/
H A DMakefile145 cram/files.o \
146 cram/mFILE.o \
156 …cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encod…
307 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
314 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
315 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
316 cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(htslib_hts_log_h) $(cram_os_h) cram/mFILE.h
318 cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram…
319 cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_…
320 cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(htslib_hts_log_h) $(cram_sam_h…
[all …]
H A Dhtslib.mk51 $(HTSDIR)/htslib/cram.h \
113 $(HTSDIR)/cram/cram.h \
121 $(HTSDIR)/cram/cram_index.c \
123 $(HTSDIR)/cram/cram_io.c \
124 $(HTSDIR)/cram/cram_io.h \
130 $(HTSDIR)/cram/files.c \
131 $(HTSDIR)/cram/mFILE.c \
132 $(HTSDIR)/cram/mFILE.h \
133 $(HTSDIR)/cram/misc.h \
136 $(HTSDIR)/cram/os.h \
[all …]
/dports/biology/vt/vt-0.57721/lib/htslib/
H A Dhtslib.mk51 $(HTSDIR)/htslib/cram.h \
110 $(HTSDIR)/cram/cram.h \
118 $(HTSDIR)/cram/cram_index.c \
120 $(HTSDIR)/cram/cram_io.c \
121 $(HTSDIR)/cram/cram_io.h \
127 $(HTSDIR)/cram/files.c \
128 $(HTSDIR)/cram/mFILE.c \
129 $(HTSDIR)/cram/mFILE.h \
130 $(HTSDIR)/cram/misc.h \
133 $(HTSDIR)/cram/os.h \
[all …]
H A DMakefile160 cram/files.o \
161 cram/mFILE.o \
171 …cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encod…
319 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
326 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
327 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
328 cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(cram_os_h) cram/mFILE.h
330 cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram…
331 cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_…
332 cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string…
[all …]
/dports/www/firefox/firefox-99.0/third_party/python/cram/cram-0.7.dist-info/
H A DRECORD1 cram/__init__.py,sha256=80M3WLqeS6MAACoIZW89KZR4bOmFm7UcpoRPF6S-8jc,172
2 cram/__main__.py,sha256=AUlczSWsDtiA6srk4dsmdsz8cZXb1QXMdPkobAR-Ex0,152
3 cram/_cli.py,sha256=aIJE2BY0djuOqgtCHe9IVUIl7Vvvk-awsksdmMd1RNc,4345
4 cram/_diff.py,sha256=pXLlKb1UgQX17ayJpPQsGoMHW7bKLcACe9KEZlnMkx0,5630
5 cram/_encoding.py,sha256=PSPdcjenMvC0wabbPhWPkCxeUcohcQ6o3Rk58AC97Uo,2990
6 cram/_main.py,sha256=5gwaBNSyKCq9bwkRLKqNXcsB5Okf0sfxDpousd51CO4,7728
8 cram/_run.py,sha256=X5fOy7TKxMdBcis0JczYZkNUoQdJ5wUqlDCM2sRJDm0,2292
9 cram/_test.py,sha256=9QYuf3DRuLs9O1QVP3MfoJlISBRfnC5ONhCL4uXGYG8,7904
10 cram/_xunit.py,sha256=KUAUokY3HhkgPYp0IjSl2m7KvztYdbwW7p1aqdaUJgA,6247
11 cram-0.7.data/scripts/cram,sha256=S3wCw9Ks2J4dtVftWZ8DU0eNtpb1ekf8Bz73Di3PvUs,112
[all …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/
H A Dhtslib.mk51 $(HTSDIR)/htslib/cram.h \
118 $(HTSDIR)/cram/cram.h \
126 $(HTSDIR)/cram/cram_index.c \
127 $(HTSDIR)/cram/cram_index.h \
128 $(HTSDIR)/cram/cram_io.c \
129 $(HTSDIR)/cram/cram_io.h \
135 $(HTSDIR)/cram/mFILE.c \
136 $(HTSDIR)/cram/mFILE.h \
137 $(HTSDIR)/cram/misc.h \
140 $(HTSDIR)/cram/os.h \
[all …]
H A DMakefile176 cram/cram_io.o \
179 cram/mFILE.o \
194 …cram/cram.h $(cram_samtools_h) $(header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/…
200 cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
356 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
359 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cra…
363 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
364 cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(htslib_hts_log_h) $(cram_os_h) cram/mFILE.h
366 cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram…
367 cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_…
[all …]
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/test/
H A Dtest.pl242 testv "./test_view $tv_args -D $cram > $cram.sam_";
246 $cram = "$bam.cram";
248 testv "./test_view $tv_args -b -D $cram > $cram.bam";
249 testv "./test_view $tv_args $cram.bam > $cram.bam.sam_";
255 testv "./test_view $tv_args -D $cram > $cram.sam_";
259 $cram = "$bam.cram";
261 testv "./test_view $tv_args -b -D $cram > $cram.bam";
262 testv "./test_view $tv_args $cram.bam > $cram.bam.sam_";
267 testv "./test_view $tv_args -t $ref -C -o VERSION=2.1 $cram > $cram.cram";
270 testv "./test_view $tv_args -t $ref -C -o VERSION=3.0 $cram.cram > $cram";
[all …]
/dports/biology/py-pysam/pysam-0.18.0/htslib/
H A Dhtslib.mk59 $(HTSSRCDIR)/htslib/cram.h \
125 $(HTSSRCDIR)/cram/cram.h \
133 $(HTSSRCDIR)/cram/cram_index.c \
134 $(HTSSRCDIR)/cram/cram_index.h \
135 $(HTSSRCDIR)/cram/cram_io.c \
136 $(HTSSRCDIR)/cram/cram_io.h \
138 $(HTSSRCDIR)/cram/cram_stats.c \
141 $(HTSSRCDIR)/cram/mFILE.c \
142 $(HTSSRCDIR)/cram/mFILE.h \
143 $(HTSSRCDIR)/cram/misc.h \
[all …]
/dports/biology/htslib/htslib-1.14/
H A Dhtslib.mk59 $(HTSSRCDIR)/htslib/cram.h \
125 $(HTSSRCDIR)/cram/cram.h \
133 $(HTSSRCDIR)/cram/cram_index.c \
134 $(HTSSRCDIR)/cram/cram_index.h \
135 $(HTSSRCDIR)/cram/cram_io.c \
136 $(HTSSRCDIR)/cram/cram_io.h \
138 $(HTSSRCDIR)/cram/cram_stats.c \
141 $(HTSSRCDIR)/cram/mFILE.c \
142 $(HTSSRCDIR)/cram/mFILE.h \
143 $(HTSSRCDIR)/cram/misc.h \
[all …]
/dports/devel/cram/cram-0.7/tests/
H A Dconfig.t1 Set up cram alias and example tests:
8 > [cram]
13 $ cram
17 $ CRAMRC=config cram
25 > [cram]
28 $ cram
29 [Uu]sage: cram \[OPTIONS\] TESTS\.\.\. (re)
35 > [cram]
38 $ cram
39 [Uu]sage: cram \[OPTIONS\] TESTS\.\.\. (re)
[all …]
H A Ddebug.t1 Set up cram alias and example tests:
8 $ cram -d -v debug.t
11 $ cram -d -q debug.t
14 $ cram -d -i debug.t
17 $ cram -d --xunit-file==cram.xml debug.t
20 $ cram -d debug.t
23 $ cram -d examples/empty.t
27 $ cram --shell-opts='-s' -d debug.t
39 $ cram -d set-x.t
46 $ cram set-x.t
H A Dusage.t1 Set up cram alias and example tests:
7 $ cram -h
8 [Uu]sage: cram \[OPTIONS\] TESTS\.\.\. (re)
25 $ cram -V
31 $ cram
32 [Uu]sage: cram \[OPTIONS\] TESTS\.\.\. (re)
34 $ cram -y -n
37 $ cram non-existent also-not-here
41 $ cram empty
44 $ cram --shell=./badsh
/dports/benchmarks/sysbench/sysbench-1.0.20/third_party/cram/tests/
H A Dconfig.t1 Set up cram alias and example tests:
8 > [cram]
13 $ cram
17 $ CRAMRC=config cram
25 > [cram]
28 $ cram
29 [Uu]sage: cram \[OPTIONS\] TESTS\.\.\. (re)
35 > [cram]
38 $ cram
39 [Uu]sage: cram \[OPTIONS\] TESTS\.\.\. (re)
[all …]
H A Ddebug.t1 Set up cram alias and example tests:
8 $ cram -d -v debug.t
11 $ cram -d -q debug.t
14 $ cram -d -i debug.t
17 $ cram -d --xunit-file==cram.xml debug.t
20 $ cram -d debug.t
23 $ cram -d examples/empty.t
27 $ cram --shell-opts='-s' -d debug.t
39 $ cram -d set-x.t
46 $ cram set-x.t
/dports/biology/vt/vt-0.57721/lib/htslib/test/
H A Dtest.pl281 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
285 $cram = "$bam.cram";
287 testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
288 testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
294 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
298 $cram = "$bam.cram";
300 testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
301 testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
306 testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=2.1 $cram > $cram.cram";
309 testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 $cram.cram > $cram";
[all …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/
H A Dtest.pl549 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
553 $cram = "$bam.cram";
555 testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
556 testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
562 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
568 testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
569 testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
581 testv $opts, "./test_view $tv_args $cram > $cram.sam_";
705 testv $opts, "./test_view -i decode_md=0 -D $cram > $cram.sam_";
711 testv $opts, "./test_view -i decode_md=0 -D $cram > $cram.sam_";
[all …]
/dports/lang/racket/racket-8.3/share/pkgs/sasl-lib/private/
H A Dcram-md5.rkt12 (struct cram-md5-client-ctx sasl-ctx (p-authcid p-password))
16 (define (make-cram-md5-client-ctx authcid password)
17 (define p-authcid (saslprep authcid #:who 'make-cram-md5-client-ctx))
18 (define p-password (string->bytes/utf-8 (saslprep password #:who 'make-cram-md5-client-ctx)))
19 (cram-md5-client-ctx #f cram-md5-client-receive-1 p-authcid p-password))
21 (define (cram-md5-client-receive-1 ctx msg)
22 (match-define (cram-md5-client-ctx _ _ p-authcid p-password) ctx)
27 (define (cram-md5-client-response authcid password challenge)
28 (define p-authcid (saslprep authcid #:who 'cram-md5-client-response))
29 (define p-password (string->bytes/utf-8 (saslprep password #:who 'cram-md5-client-response)))
/dports/biology/htslib/htslib-1.14/test/
H A Dtest.pl578 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
585 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
590 $cram = "$bam.cram";
592 testv $opts, "./test_view $tv_args $cram > $cram.bam.sam_";
598 testv $opts, "./test_view $tv_args $cram.ms > $cram.sam_";
611 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
623 testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
744 $cram = "$base.tmp.cram";
749 testv $opts, "./test_view -i decode_md=0 -D $cram > $cram.sam_";
755 testv $opts, "./test_view -i decode_md=0 -D $cram > $cram.sam_";
[all …]
/dports/biology/pbbam/pbbam-0.18.0/tests/src/
H A Dmeson.build60 # cram files
61 pbbam_cram_bam2sam_t_in = files('cram/bam2sam.t.in')
62 pbbam_cram_pbindexdump_json_t_in = files('cram/pbindexdump_json.t.in')
63 pbbam_cram_pbindexdump_cpp_t_in = files('cram/pbindexdump_cpp.t.in')
64 pbbam_cram_pbmerge_pacbio_ordering_t_in = files('cram/pbmerge_pacbio_ordering.t.in')
65 pbbam_cram_pbmerge_aligned_ordering_t_in = files('cram/pbmerge_aligned_ordering.t.in')
66 pbbam_cram_pbmerge_mixed_ordering_t_in = files('cram/pbmerge_mixed_ordering.t.in')
67 pbbam_cram_pbmerge_dataset_t_in = files('cram/pbmerge_dataset.t.in')
68 pbbam_cram_pbmerge_fofn_t_in = files('cram/pbmerge_fofn.t.in')
69 pbbam_cram_pbbamify_t_in = files('cram/pbbamify.t.in')
/dports/security/courierpasswd/courierpasswd-1.1.3/
H A Dcourierpasswd.c119 if (!strncmp(cram, "md5", 3)){ in findcramtype()
121 } else if (!strncmp(cram, "sha1", 4)){ in findcramtype()
123 } else if (!strncmp(cram, "sha256", 6)){ in findcramtype()
149 char cram[MAX_LEN_SERVICE]; in main() local
155 *service = *cram = *authtype_cram = 0; in main()
160 strlcpy(cram, "md5", 4); in main()
194 n = strlcpy(cram, optarg, sizeof(cram)); in main()
195 if (n >= sizeof(cram)){ in main()
201 n = findcramtype(cram, authtype_cram); in main()
244 n = findcramtype(cram, authtype_cram); in main()
[all …]

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