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commit eeb4b225c70ae3f09ef2986f8530140c730bcac3 Merge: a7e257d 258b4e6 Author: John Marshall <[email protected]> Date: Thu Aug 21 17:18:30 2014 +0100 Merge minimal MD5 reference area for mpileup tests Provide a local reference area via $REF_PATH for mpileup/regression.sh tests (cf 38eda28b81fd3c176f90a0f03d2645fc891167f0's commit message). (Note that these MD5 files are truncated versions of their full sequences; just enough to pass the tests.) Set REF_PATH to an empty value (but not the empty string, as that produces the default setting), or in general to point within the test suite, for tests that exercise it -- currently test.pl and regression.sh. This makes the test suite self-contained for reference areas, and in particular prevents travis build testing from trying to access the EBI reference server. Fixes #279. Makefile | 7 +++++-- test/mpileup/md5/02099b2aad2cfe707759353724fb40ae | 1 + test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d | 1 + test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de | 1 + test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc | 1 + test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 | 1 + test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e | 1 + test/mpileup/regression.sh | 8 ++++++++ 8 files changed, 19 insertions(+), 2 deletions(-) diff --cc Makefile index c621353,d1a4b34..85e79d7 --- a/Makefile +++ b/Makefile @@@ -176,17 -175,17 +176,20 @@@ stats.o: stats.c $(sam_h) sam_header.h # test programs ++# For tests that might use it, set $REF_PATH explicitly to use only reference ++# areas within the test suite (or set it to ':' to use no reference areas). ++# (regression.sh sets $REF_PATH to a subdirectory itself.) check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - test/test.pl --exec bgzip=$(BGZIP) - REF_PATH=/does_not_exist test/test.pl --exec bgzip=$(BGZIP) - REF_PATH=/does_not_exist test/merge/test_bam_translate test/merge/test_bam_translate.tmp - REF_PATH=/does_not_exist test/merge/test_pretty_header - REF_PATH=/does_not_exist test/merge/test_rtrans_build - REF_PATH=/does_not_exist test/merge/test_trans_tbl_init ++ REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_pretty_header + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init - if [ -n "$$REF_PATH" ]; then cd test/mpileup && ./regression.sh; fi + cd test/mpileup && ./regression.sh - REF_PATH=/does_not_exist test/split/test_count_rg - REF_PATH=/does_not_exist test/split/test_expand_format_string - REF_PATH=/does_not_exist test/split/test_filter_header_rg - REF_PATH=/does_not_exist test/split/test_parse_args + test/split/test_count_rg + test/split/test_expand_format_string + test/split/test_filter_header_rg + test/split/test_parse_args test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
