[med-svn] [python-pysam] branch master updated (f579596 -> 5eb39c8)
Jorge Soares
jssoares-guest at moszumanska.debian.org
Fri Nov 28 09:08:45 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a change to branch master
in repository python-pysam.
from f579596 concluding merge
new 5eb39c8 Added the tests directory as I think this will solve all the non building problems
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/rules | 12 +-
tests/AlignmentFile_test.py | 2057 +++
tests/SamFile_test.py | 1927 +++
tests/TestUtils.py | 52 +
tests/_compile_test.pyx | 29 +
tests/_compile_test.pyxbld | 8 +
tests/_cython_flagstat.pyx | 18 +
tests/_cython_flagstat.pyxbld | 8 +
tests/compile_test.py | 46 +
tests/cython_flagstat.py | 12 +
tests/faidx_test.py | 87 +
tests/pysam_data/Makefile | 63 +
tests/pysam_data/ex1.bed | 2 +
tests/pysam_data/ex1.fa | 56 +
tests/pysam_data/ex1.fq | 13080 ++++++++++++++++++++
tests/pysam_data/ex1.sam.gz | Bin 0 -> 113194 bytes
tests/pysam_data/ex10.sam | 16 +
tests/pysam_data/ex3.sam | 13 +
tests/pysam_data/ex4.sam | 9 +
tests/pysam_data/ex5.sam | 5 +
tests/pysam_data/ex6.sam | 5 +
tests/pysam_data/ex7.sam.donottest | 2 +
tests/pysam_data/ex8.sam | 3 +
tests/pysam_data/ex9_fail.sam | 1022 ++
tests/pysam_data/ex9_nofail.sam | 1021 ++
tests/pysam_data/example_btag.sam | 6 +
tests/pysam_data/example_empty_header.sam | 321 +
tests/pysam_data/example_unmapped_reads_no_sq.sam | 3 +
tests/pysam_data/example_user_header.sam | 8 +
tests/pysam_data/issue100.sam | 27 +
tests/pysam_data/rg_with_tab.sam | 3273 +++++
tests/pysam_data/softclip.sam | 6 +
tests/pysam_data/tag_bug.sam | 16 +
tests/pysam_data/test.gtf | 10 +
tests/pysam_data/test.gtf.gz | Bin 0 -> 311 bytes
tests/pysam_data/test_unaligned.sam | 6 +
tests/python_flagstat.py | 13 +
tests/refactoring.pl | 60 +
tests/refactoring.txt | 198 +
tests/samtools_test.py | 383 +
tests/tabix_data/example.bed.gz | Bin 0 -> 819 bytes
tests/tabix_data/example.bed.gz.tbi | Bin 0 -> 192 bytes
tests/tabix_data/example.gtf.gz | Bin 0 -> 3778 bytes
tests/tabix_data/example.gtf.gz.tbi | Bin 0 -> 196 bytes
tests/tabix_data/example.sam.gz | Bin 0 -> 398 bytes
tests/tabix_data/example.sam.gz.tbi | Bin 0 -> 128 bytes
tests/tabix_data/example.vcf.gz | Bin 0 -> 328 bytes
tests/tabix_data/example.vcf.gz.tbi | Bin 0 -> 182 bytes
tests/tabix_data/example.vcf40 | 23 +
tests/tabix_data/example_badcomments.bed.gz | Bin 0 -> 879 bytes
tests/tabix_data/example_badcomments.bed.gz.tbi | Bin 0 -> 194 bytes
tests/tabix_data/example_badcomments.gtf.gz | Bin 0 -> 3825 bytes
tests/tabix_data/example_badcomments.gtf.gz.tbi | Bin 0 -> 198 bytes
tests/tabix_data/example_badcomments.sam.gz | Bin 0 -> 398 bytes
tests/tabix_data/example_badcomments.sam.gz.tbi | Bin 0 -> 128 bytes
tests/tabix_data/example_badcomments.vcf.gz | Bin 0 -> 753 bytes
tests/tabix_data/example_badcomments.vcf.gz.tbi | Bin 0 -> 186 bytes
tests/tabix_data/example_comments.bed.gz | Bin 0 -> 849 bytes
tests/tabix_data/example_comments.bed.gz.tbi | Bin 0 -> 194 bytes
tests/tabix_data/example_comments.gtf.gz | Bin 0 -> 3792 bytes
tests/tabix_data/example_comments.gtf.gz.tbi | Bin 0 -> 198 bytes
tests/tabix_data/example_comments.sam.gz | Bin 0 -> 398 bytes
tests/tabix_data/example_comments.sam.gz.tbi | Bin 0 -> 128 bytes
tests/tabix_data/example_comments.vcf.gz | Bin 0 -> 753 bytes
tests/tabix_data/example_comments.vcf.gz.tbi | Bin 0 -> 186 bytes
tests/tabix_data/example_unicode.vcf | 23 +
tests/tabix_data/gtf_toofew_fields.gtf.gz | Bin 0 -> 400 bytes
tests/tabix_data/gtf_toomany_fields.gtf.gz | Bin 0 -> 400 bytes
tests/tabix_data/gtf_wrong_fields.gtf.gz | Bin 0 -> 400 bytes
tests/tabix_data/vcf/10.vcf | 84 +
tests/tabix_data/vcf/11.vcf | 216 +
tests/tabix_data/vcf/12.vcf | 1000 ++
tests/tabix_data/vcf/13.vcf | 220 +
tests/tabix_data/vcf/15.vcf | 317 +
tests/tabix_data/vcf/16.vcf | 369 +
tests/tabix_data/vcf/18.vcf | 1000 ++
tests/tabix_data/vcf/2.vcf | 334 +
tests/tabix_data/vcf/20.vcf | 307 +
tests/tabix_data/vcf/21.vcf | 310 +
tests/tabix_data/vcf/22.vcf | 1000 ++
tests/tabix_data/vcf/23.vcf | 419 +
tests/tabix_data/vcf/24.vcf | 724 ++
tests/tabix_data/vcf/3.vcf | 1000 ++
tests/tabix_data/vcf/4.vcf | 318 +
tests/tabix_data/vcf/5.vcf | 1000 ++
tests/tabix_data/vcf/6.vcf | 278 +
tests/tabix_data/vcf/7.vcf | 317 +
tests/tabix_data/vcf/8.vcf | 84 +
tests/tabix_data/vcf/9.vcf | 1000 ++
tests/tabix_data/vcf/README.txt | 11 +
tests/tabix_data/vcf/issue85.vcf | 26 +
tests/tabix_test.py | 1020 ++
92 files changed, 35277 insertions(+), 6 deletions(-)
create mode 100644 tests/AlignmentFile_test.py
create mode 100644 tests/SamFile_test.py
create mode 100644 tests/TestUtils.py
create mode 100644 tests/_compile_test.pyx
create mode 100644 tests/_compile_test.pyxbld
create mode 100644 tests/_cython_flagstat.pyx
create mode 100644 tests/_cython_flagstat.pyxbld
create mode 100644 tests/compile_test.py
create mode 100644 tests/cython_flagstat.py
create mode 100644 tests/faidx_test.py
create mode 100644 tests/pysam_data/Makefile
create mode 100644 tests/pysam_data/ex1.bed
create mode 100644 tests/pysam_data/ex1.fa
create mode 100644 tests/pysam_data/ex1.fq
create mode 100644 tests/pysam_data/ex1.sam.gz
create mode 100644 tests/pysam_data/ex10.sam
create mode 100644 tests/pysam_data/ex3.sam
create mode 100644 tests/pysam_data/ex4.sam
create mode 100644 tests/pysam_data/ex5.sam
create mode 100644 tests/pysam_data/ex6.sam
create mode 100644 tests/pysam_data/ex7.sam.donottest
create mode 100644 tests/pysam_data/ex8.sam
create mode 100644 tests/pysam_data/ex9_fail.sam
create mode 100644 tests/pysam_data/ex9_nofail.sam
create mode 100644 tests/pysam_data/example_btag.sam
create mode 100644 tests/pysam_data/example_empty_header.sam
create mode 100644 tests/pysam_data/example_unmapped_reads_no_sq.sam
create mode 100644 tests/pysam_data/example_user_header.sam
create mode 100644 tests/pysam_data/issue100.sam
create mode 100644 tests/pysam_data/rg_with_tab.sam
create mode 100644 tests/pysam_data/softclip.sam
create mode 100644 tests/pysam_data/tag_bug.sam
create mode 100644 tests/pysam_data/test.gtf
create mode 100644 tests/pysam_data/test.gtf.gz
create mode 100644 tests/pysam_data/test_unaligned.sam
create mode 100644 tests/python_flagstat.py
create mode 100644 tests/refactoring.pl
create mode 100644 tests/refactoring.txt
create mode 100644 tests/samtools_test.py
create mode 100644 tests/tabix_data/example.bed.gz
create mode 100644 tests/tabix_data/example.bed.gz.tbi
create mode 100644 tests/tabix_data/example.gtf.gz
create mode 100644 tests/tabix_data/example.gtf.gz.tbi
create mode 100644 tests/tabix_data/example.sam.gz
create mode 100644 tests/tabix_data/example.sam.gz.tbi
create mode 100644 tests/tabix_data/example.vcf.gz
create mode 100644 tests/tabix_data/example.vcf.gz.tbi
create mode 100644 tests/tabix_data/example.vcf40
create mode 100644 tests/tabix_data/example_badcomments.bed.gz
create mode 100644 tests/tabix_data/example_badcomments.bed.gz.tbi
create mode 100644 tests/tabix_data/example_badcomments.gtf.gz
create mode 100644 tests/tabix_data/example_badcomments.gtf.gz.tbi
create mode 100644 tests/tabix_data/example_badcomments.sam.gz
create mode 100644 tests/tabix_data/example_badcomments.sam.gz.tbi
create mode 100644 tests/tabix_data/example_badcomments.vcf.gz
create mode 100644 tests/tabix_data/example_badcomments.vcf.gz.tbi
create mode 100644 tests/tabix_data/example_comments.bed.gz
create mode 100644 tests/tabix_data/example_comments.bed.gz.tbi
create mode 100644 tests/tabix_data/example_comments.gtf.gz
create mode 100644 tests/tabix_data/example_comments.gtf.gz.tbi
create mode 100644 tests/tabix_data/example_comments.sam.gz
create mode 100644 tests/tabix_data/example_comments.sam.gz.tbi
create mode 100644 tests/tabix_data/example_comments.vcf.gz
create mode 100644 tests/tabix_data/example_comments.vcf.gz.tbi
create mode 100644 tests/tabix_data/example_unicode.vcf
create mode 100644 tests/tabix_data/gtf_toofew_fields.gtf.gz
create mode 100644 tests/tabix_data/gtf_toomany_fields.gtf.gz
create mode 100644 tests/tabix_data/gtf_wrong_fields.gtf.gz
create mode 100644 tests/tabix_data/vcf/10.vcf
create mode 100644 tests/tabix_data/vcf/11.vcf
create mode 100644 tests/tabix_data/vcf/12.vcf
create mode 100644 tests/tabix_data/vcf/13.vcf
create mode 100644 tests/tabix_data/vcf/15.vcf
create mode 100644 tests/tabix_data/vcf/16.vcf
create mode 100644 tests/tabix_data/vcf/18.vcf
create mode 100644 tests/tabix_data/vcf/2.vcf
create mode 100644 tests/tabix_data/vcf/20.vcf
create mode 100644 tests/tabix_data/vcf/21.vcf
create mode 100644 tests/tabix_data/vcf/22.vcf
create mode 100644 tests/tabix_data/vcf/23.vcf
create mode 100644 tests/tabix_data/vcf/24.vcf
create mode 100644 tests/tabix_data/vcf/3.vcf
create mode 100644 tests/tabix_data/vcf/4.vcf
create mode 100644 tests/tabix_data/vcf/5.vcf
create mode 100644 tests/tabix_data/vcf/6.vcf
create mode 100644 tests/tabix_data/vcf/7.vcf
create mode 100644 tests/tabix_data/vcf/8.vcf
create mode 100644 tests/tabix_data/vcf/9.vcf
create mode 100644 tests/tabix_data/vcf/README.txt
create mode 100644 tests/tabix_data/vcf/issue85.vcf
create mode 100644 tests/tabix_test.py
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