[med-svn] samtools 11/11: Merge minimal MD5 reference area for mpileup tests

[Charles Plessy]

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plessy pushed a commit to branch develop
in repository samtools.

commit eeb4b225c70ae3f09ef2986f8530140c730bcac3
Merge: a7e257d 258b4e6
Author: John Marshall <jm18 at sanger.ac.uk>
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)

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