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commit 258b4e60661f687d9ff509fc2b97fe00b37ebb89 Author: James Bonfield <[email protected]> Date: Tue Aug 19 11:27:35 2014 +0100 Modified the mpileup tests to have local copies of appropriate reference sequences. All other tests already had this (but accidentally escaped in some circumstances). Added a non-existant REF_PATH= to the tests to prevent it using the default search path and escaping off to the EBI. See https://github.com/samtools/samtools/issues/279 --- Makefile | 20 ++++++++++---------- 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, 24 insertions(+), 10 deletions(-) diff --git a/Makefile b/Makefile index e110b31..d1a4b34 100644 --- a/Makefile +++ b/Makefile @@ -176,16 +176,16 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib # test programs check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) - test/test.pl --exec bgzip=$(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 - test/split/test_count_rg - test/split/test_expand_format_string - test/split/test_filter_header_rg - test/split/test_parse_args + 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 + 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/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) diff --git a/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae b/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae new file mode 100644 index 0000000..68413b9 --- /dev/null +++ b/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae @@ -0,0 +1 @@ +CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGAAGAGACCAAACCGAAAAATCAATTTTTTAAACGAAAAATCAATGTTTTA \ No newline at end of file diff --git a/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d b/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d new file mode 100644 index 0000000..508edec --- /dev/null +++ b/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d @@ -0,0 +1 @@ +CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAAGCGCGAAATCCTATGAAATTTCAAGGATTTATAACTTTTTGAGTCCGAAAAGAGTCGGAAATCAGAT \ No newline at end of file diff --git a/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de b/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de new file mode 100644 index 0000000..e06cdfd --- /dev/null +++ b/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de @@ -0,0 +1 @@ +AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATG [...] \ No newline at end of file diff --git a/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc b/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc new file mode 100644 index 0000000..d85cde7 --- /dev/null +++ b/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc @@ -0,0 +1 @@ +GAATTCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCATAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCATAAGCCTAAGCCT \ No newline at end of file diff --git a/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 b/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 new file mode 100644 index 0000000..242acd2 --- /dev/null +++ b/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 @@ -0,0 +1 @@ +GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGC \ No newline at end of file diff --git a/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e b/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e new file mode 100644 index 0000000..b04ec63 --- /dev/null +++ b/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e @@ -0,0 +1 @@ +CCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAATAGTGACTCTGGCAGTTCTCTAAAA \ No newline at end of file diff --git a/test/mpileup/regression.sh b/test/mpileup/regression.sh index 1200bca..4360e6e 100755 --- a/test/mpileup/regression.sh +++ b/test/mpileup/regression.sh @@ -25,6 +25,14 @@ # allow cmd|md5sum to set $? to 1 if cmd fails but md5sum works set +o | grep pipefail >/dev/null && set -o pipefail +# Use a local MD5 directory, which also has the benefit of overriding the +# inbuilt REF_PATH removing the external dependency on EBI. +# +# Note that these MD5 files are truncated versions of their full sequences; +# just enough to pass the tests. +REF_PATH=`pwd`/md5 +export REF_PATH + # Executes a single test and compares against the expected output run_test() { p=$1; shift -- 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
