[med-svn] samtools 06/11: Modified the mpileup tests to have local copies of appropriate reference sequences. All other tests already had this (but accidentally escaped in some circumstances).
Charles Plessy
plessy at moszumanska.debian.org
Thu Aug 21 22:58:53 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch develop
in repository samtools.
commit 258b4e60661f687d9ff509fc2b97fe00b37ebb89
Author: James Bonfield <jkb at sanger.ac.uk>
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
More information about the debian-med-commit
mailing list