[med-svn] [python-pysam] branch upstream updated (3a45c2d -> 5128bf9)
Jorge Soares
jssoares-guest at moszumanska.debian.org
Fri Nov 28 09:30:08 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a change to branch upstream
in repository python-pysam.
from 3a45c2d Imported Upstream version 0.8.1
new e061ec4 Imported Upstream version 0.8.1
new 5128bf9 Imported Upstream version 0.8.1
The 2 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:
.gitignore | 77 +
.hgignore | 7 +
.hgtags | 4 +
.travis.yml | 14 +
AUTHORS | 32 +
PKG-INFO | 16 -
benchmark/tabix_bench.py | 76 +
benchmark/windows_small.bed | 100000 ++++++++++++++++++
benchmark/windows_small.bed.gz | Bin 0 -> 459587 bytes
benchmark/windows_small.bed.gz.tbi | Bin 0 -> 34590 bytes
doc/out | 30 -
htslib/INSTALL | 25 +
htslib/LICENSE | 69 +
htslib/Makefile | 337 +
htslib/README | 5 +
htslib/faidx.5 | 147 +
htslib/htslib.mk | 144 +
htslib/htslib.pc.in | 10 +
htslib/htslib_vars.mk | 38 +
htslib/sam.5 | 68 +
htslib/tabix.1 | 155 +
htslib/test/aux#aux.sam | 5 +
htslib/test/aux.fa | 2 +
htslib/test/aux.fa.fai | 1 +
htslib/test/c1#bounds.sam | 4 +
htslib/test/c1#clip.sam | 8 +
htslib/test/c1#pad1.sam | 10 +
htslib/test/c1#pad2.sam | 14 +
htslib/test/c1#pad3.sam | 14 +
htslib/test/c1.fa | 2 +
htslib/test/c1.fa.fai | 1 +
htslib/test/ce#1.sam | 2 +
htslib/test/ce#2.sam | 3 +
htslib/test/ce#5.sam | 11 +
htslib/test/ce#5b.sam | 12 +
htslib/test/ce#large_seq.sam | 3 +
htslib/test/ce#tag_depadded.sam | 11 +
htslib/test/ce#tag_padded.sam | 11 +
htslib/test/ce#unmap.sam | 6 +
htslib/test/ce#unmap1.sam | 20 +
htslib/test/ce#unmap2.sam | 29 +
htslib/test/ce.fa | 20803 ++++
htslib/test/ce.fa.fai | 7 +
htslib/test/compare_sam.pl | 172 +
htslib/test/fieldarith.c | 72 +
htslib/test/fieldarith.sam | 15 +
htslib/test/hfile.c | 204 +
htslib/test/sam.c | 143 +
htslib/test/test-vcf-api.c | 235 +
htslib/test/test-vcf-api.out | 28 +
htslib/test/test-vcf-sweep.c | 112 +
htslib/test/test-vcf-sweep.out | 4 +
htslib/test/test.pl | 202 +
htslib/test/test_view.c | 151 +
htslib/test/test_view.pl | 71 +
KNOWN_BUGS => htslib/test/xx#blank.sam | 0
htslib/test/xx#large_aux.sam | 4 +
htslib/test/xx#large_aux2.sam | 11 +
htslib/test/xx#minimal.sam | 10 +
htslib/test/xx#pair.sam | 7 +
htslib/test/xx#rg.sam | 13 +
htslib/test/xx#triplet.sam | 7 +
htslib/test/xx#unsorted.sam | 8 +
htslib/test/xx.fa | 5 +
htslib/test/xx.fa.fai | 2 +
htslib/vcf.5 | 120 +
install-CGAT-tools.sh | 281 +
pysam.egg-info/PKG-INFO | 16 -
pysam.egg-info/SOURCES.txt | 204 -
pysam.egg-info/dependency_links.txt | 1 -
pysam.egg-info/not-zip-safe | 1 -
pysam.egg-info/top_level.txt | 1 -
pysam/TabProxies.c | 14076 ---
pysam/{cvcf.pyx => VCF.py.obsolete} | 356 +-
pysam/alternatives.py.obsolete | 82 +
pysam/calignmentfile.c | 48377 ---------
pysam/cfaidx.c | 8717 --
pysam/chtslib.c | 3162 -
pysam/csamfile.c | 2876 -
pysam/csamtools.c | 6962 --
pysam/ctabix.c | 15462 ---
pysam/cvcf.c | 30127 ------
requires.txt | 1 +
samtools/{bam.c.pysam.c => bam.c} | 4 +-
samtools/{bam2bcf.c.pysam.c => bam2bcf.c} | 10 +-
.../{bam2bcf_indel.c.pysam.c => bam2bcf_indel.c} | 22 +-
samtools/{bam2depth.c.pysam.c => bam2depth.c} | 22 +-
samtools/{bam_aux.c.pysam.c => bam_aux.c} | 2 -
samtools/{bam_cat.c.pysam.c => bam_cat.c} | 16 +-
samtools/{bam_color.c.pysam.c => bam_color.c} | 2 -
samtools/bam_flags.c | 68 +
samtools/{bam_import.c.pysam.c => bam_import.c} | 4 +-
samtools/{bam_index.c.pysam.c => bam_index.c} | 12 +-
samtools/{bam_lpileup.c.pysam.c => bam_lpileup.c} | 12 +-
samtools/{bam_mate.c.pysam.c => bam_mate.c} | 30 +-
samtools/{bam_md.c.pysam.c => bam_md.c} | 32 +-
samtools/{bam_plbuf.c.pysam.c => bam_plbuf.c} | 2 -
samtools/{bam_plcmd.c.pysam.c => bam_plcmd.c} | 52 +-
.../{bam_reheader.c.pysam.c => bam_reheader.c} | 8 +-
samtools/{bam_rmdup.c.pysam.c => bam_rmdup.c} | 20 +-
samtools/{bam_rmdupse.c.pysam.c => bam_rmdupse.c} | 4 +-
samtools/{bam_sort.c.pysam.c => bam_sort.c} | 52 +-
samtools/{bam_split.c.pysam.c => bam_split.c} | 38 +-
samtools/{bam_stat.c.pysam.c => bam_stat.c} | 6 +-
samtools/{bam_tview.c.pysam.c => bam_tview.c} | 16 +-
...m_tview_curses.c.pysam.c => bam_tview_curses.c} | 4 +-
.../{bam_tview_html.c.pysam.c => bam_tview_html.c} | 6 +-
samtools/{bamshuf.c.pysam.c => bamshuf.c} | 4 +-
samtools/{bedcov.c.pysam.c => bedcov.c} | 8 +-
samtools/{bedidx.c.pysam.c => bedidx.c} | 6 +-
samtools/{cut_target.c.pysam.c => cut_target.c} | 6 +-
samtools/{errmod.c.pysam.c => errmod.c} | 2 -
samtools/{faidx.c.pysam.c => faidx.c} | 10 +-
samtools/{kaln.c.pysam.c => kaln.c} | 2 -
samtools/misc/{ace2sam.c.pysam.c => ace2sam.c} | 30 +-
samtools/misc/{md5.c.pysam.c => md5.c} | 4 +-
samtools/{padding.c.pysam.c => padding.c} | 90 +-
samtools/{phase.c.pysam.c => phase.c} | 26 +-
samtools/{sam.c.pysam.c => sam.c} | 10 +-
samtools/{sam_header.c.pysam.c => sam_header.c} | 8 +-
samtools/{sam_view.c.pysam.c => sam_view.c} | 92 +-
samtools/{sample.c.pysam.c => sample.c} | 2 -
samtools/{stats.c.pysam.c => stats.c} | 12 +-
samtools/{stats_isize.c.pysam.c => stats_isize.c} | 4 +-
samtools/test/merge/test_bam_translate.c | 591 +
samtools/test/merge/test_bam_translate.c.pysam.c | 593 +
samtools/test/merge/test_pretty_header.c | 87 +
samtools/test/merge/test_pretty_header.c.pysam.c | 89 +
samtools/test/merge/test_rtrans_build.c | 118 +
samtools/test/merge/test_rtrans_build.c.pysam.c | 120 +
samtools/test/merge/test_trans_tbl_init.c | 471 +
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 473 +
samtools/test/split/test_count_rg.c | 124 +
samtools/test/split/test_count_rg.c.pysam.c | 126 +
samtools/test/split/test_expand_format_string.c | 124 +
.../test/split/test_expand_format_string.c.pysam.c | 126 +
samtools/test/split/test_filter_header_rg.c | 191 +
.../test/split/test_filter_header_rg.c.pysam.c | 193 +
samtools/test/split/test_parse_args.c | 215 +
samtools/test/split/test_parse_args.c.pysam.c | 217 +
samtools/test/{test.c.pysam.c => test.c} | 4 +-
samtools/test/tview/test_get_rg_sample.c | 81 +
samtools/test/tview/test_get_rg_sample.c.pysam.c | 83 +
save/example.py | 79 +
save/pysam_bench.py | 63 +
save/pysam_test2.6.py | 1607 +
save/pysam_test_stdin.py | 10 +
save/pysam_testpp.py | 13 +
save/segfault_tests.py | 37 +
save/vcf_test.py | 123 +
setup.cfg | 6 -
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 +
win32/getopt.c | 1261 +
win32/getopt.h | 187 +
win32/stdint.h | 799 +
win32/unistd.h | 26 +
246 files changed, 168151 insertions(+), 130648 deletions(-)
create mode 100644 .gitignore
create mode 100644 .hgignore
create mode 100644 .hgtags
create mode 100644 .travis.yml
create mode 100644 AUTHORS
delete mode 100644 PKG-INFO
create mode 100644 benchmark/tabix_bench.py
create mode 100644 benchmark/windows_small.bed
create mode 100644 benchmark/windows_small.bed.gz
create mode 100644 benchmark/windows_small.bed.gz.tbi
delete mode 100644 doc/out
create mode 100644 htslib/INSTALL
create mode 100644 htslib/LICENSE
create mode 100644 htslib/Makefile
create mode 100644 htslib/README
create mode 100644 htslib/faidx.5
create mode 100644 htslib/htslib.mk
create mode 100644 htslib/htslib.pc.in
create mode 100644 htslib/htslib_vars.mk
create mode 100644 htslib/sam.5
create mode 100644 htslib/tabix.1
create mode 100644 htslib/test/aux#aux.sam
create mode 100644 htslib/test/aux.fa
create mode 100644 htslib/test/aux.fa.fai
create mode 100644 htslib/test/c1#bounds.sam
create mode 100644 htslib/test/c1#clip.sam
create mode 100644 htslib/test/c1#pad1.sam
create mode 100644 htslib/test/c1#pad2.sam
create mode 100644 htslib/test/c1#pad3.sam
create mode 100644 htslib/test/c1.fa
create mode 100644 htslib/test/c1.fa.fai
create mode 100644 htslib/test/ce#1.sam
create mode 100644 htslib/test/ce#2.sam
create mode 100644 htslib/test/ce#5.sam
create mode 100644 htslib/test/ce#5b.sam
create mode 100644 htslib/test/ce#large_seq.sam
create mode 100644 htslib/test/ce#tag_depadded.sam
create mode 100644 htslib/test/ce#tag_padded.sam
create mode 100644 htslib/test/ce#unmap.sam
create mode 100644 htslib/test/ce#unmap1.sam
create mode 100644 htslib/test/ce#unmap2.sam
create mode 100644 htslib/test/ce.fa
create mode 100644 htslib/test/ce.fa.fai
create mode 100755 htslib/test/compare_sam.pl
create mode 100644 htslib/test/fieldarith.c
create mode 100644 htslib/test/fieldarith.sam
create mode 100644 htslib/test/hfile.c
create mode 100644 htslib/test/sam.c
create mode 100644 htslib/test/test-vcf-api.c
create mode 100644 htslib/test/test-vcf-api.out
create mode 100644 htslib/test/test-vcf-sweep.c
create mode 100644 htslib/test/test-vcf-sweep.out
create mode 100755 htslib/test/test.pl
create mode 100644 htslib/test/test_view.c
create mode 100755 htslib/test/test_view.pl
copy KNOWN_BUGS => htslib/test/xx#blank.sam (100%)
create mode 100644 htslib/test/xx#large_aux.sam
create mode 100644 htslib/test/xx#large_aux2.sam
create mode 100644 htslib/test/xx#minimal.sam
create mode 100644 htslib/test/xx#pair.sam
create mode 100644 htslib/test/xx#rg.sam
create mode 100644 htslib/test/xx#triplet.sam
create mode 100644 htslib/test/xx#unsorted.sam
create mode 100644 htslib/test/xx.fa
create mode 100644 htslib/test/xx.fa.fai
create mode 100644 htslib/vcf.5
create mode 100755 install-CGAT-tools.sh
delete mode 100644 pysam.egg-info/PKG-INFO
delete mode 100644 pysam.egg-info/SOURCES.txt
delete mode 100644 pysam.egg-info/dependency_links.txt
delete mode 100644 pysam.egg-info/not-zip-safe
delete mode 100644 pysam.egg-info/top_level.txt
delete mode 100644 pysam/TabProxies.c
copy pysam/{cvcf.pyx => VCF.py.obsolete} (79%)
create mode 100644 pysam/alternatives.py.obsolete
delete mode 100644 pysam/calignmentfile.c
delete mode 100644 pysam/cfaidx.c
delete mode 100644 pysam/chtslib.c
delete mode 100644 pysam/csamfile.c
delete mode 100644 pysam/csamtools.c
delete mode 100644 pysam/ctabix.c
delete mode 100644 pysam/cvcf.c
create mode 100644 requires.txt
copy samtools/{bam.c.pysam.c => bam.c} (98%)
copy samtools/{bam2bcf.c.pysam.c => bam2bcf.c} (98%)
copy samtools/{bam2bcf_indel.c.pysam.c => bam2bcf_indel.c} (95%)
copy samtools/{bam2depth.c.pysam.c => bam2depth.c} (91%)
copy samtools/{bam_aux.c.pysam.c => bam_aux.c} (99%)
copy samtools/{bam_cat.c.pysam.c => bam_cat.c} (86%)
copy samtools/{bam_color.c.pysam.c => bam_color.c} (99%)
create mode 100644 samtools/bam_flags.c
copy samtools/{bam_import.c.pysam.c => bam_import.c} (95%)
copy samtools/{bam_index.c.pysam.c => bam_index.c} (89%)
copy samtools/{bam_lpileup.c.pysam.c => bam_lpileup.c} (96%)
copy samtools/{bam_mate.c.pysam.c => bam_mate.c} (91%)
copy samtools/{bam_md.c.pysam.c => bam_md.c} (91%)
copy samtools/{bam_plbuf.c.pysam.c => bam_plbuf.c} (99%)
copy samtools/{bam_plcmd.c.pysam.c => bam_plcmd.c} (93%)
copy samtools/{bam_reheader.c.pysam.c => bam_reheader.c} (90%)
copy samtools/{bam_rmdup.c.pysam.c => bam_rmdup.c} (89%)
copy samtools/{bam_rmdupse.c.pysam.c => bam_rmdupse.c} (97%)
copy samtools/{bam_sort.c.pysam.c => bam_sort.c} (95%)
copy samtools/{bam_split.c.pysam.c => bam_split.c} (91%)
copy samtools/{bam_stat.c.pysam.c => bam_stat.c} (97%)
copy samtools/{bam_tview.c.pysam.c => bam_tview.c} (96%)
copy samtools/{bam_tview_curses.c.pysam.c => bam_tview_curses.c} (99%)
copy samtools/{bam_tview_html.c.pysam.c => bam_tview_html.c} (98%)
copy samtools/{bamshuf.c.pysam.c => bamshuf.c} (99%)
copy samtools/{bedcov.c.pysam.c => bedcov.c} (94%)
copy samtools/{bedidx.c.pysam.c => bedidx.c} (97%)
copy samtools/{cut_target.c.pysam.c => cut_target.c} (96%)
copy samtools/{errmod.c.pysam.c => errmod.c} (99%)
copy samtools/{faidx.c.pysam.c => faidx.c} (92%)
copy samtools/{kaln.c.pysam.c => kaln.c} (99%)
copy samtools/misc/{ace2sam.c.pysam.c => ace2sam.c} (90%)
copy samtools/misc/{md5.c.pysam.c => md5.c} (99%)
copy samtools/{padding.c.pysam.c => padding.c} (79%)
copy samtools/{phase.c.pysam.c => phase.c} (96%)
copy samtools/{sam.c.pysam.c => sam.c} (90%)
copy samtools/{sam_header.c.pysam.c => sam_header.c} (99%)
copy samtools/{sam_view.c.pysam.c => sam_view.c} (85%)
copy samtools/{sample.c.pysam.c => sample.c} (99%)
copy samtools/{stats.c.pysam.c => stats.c} (99%)
copy samtools/{stats_isize.c.pysam.c => stats_isize.c} (98%)
create mode 100644 samtools/test/merge/test_bam_translate.c
create mode 100644 samtools/test/merge/test_bam_translate.c.pysam.c
create mode 100644 samtools/test/merge/test_pretty_header.c
create mode 100644 samtools/test/merge/test_pretty_header.c.pysam.c
create mode 100644 samtools/test/merge/test_rtrans_build.c
create mode 100644 samtools/test/merge/test_rtrans_build.c.pysam.c
create mode 100644 samtools/test/merge/test_trans_tbl_init.c
create mode 100644 samtools/test/merge/test_trans_tbl_init.c.pysam.c
create mode 100644 samtools/test/split/test_count_rg.c
create mode 100644 samtools/test/split/test_count_rg.c.pysam.c
create mode 100644 samtools/test/split/test_expand_format_string.c
create mode 100644 samtools/test/split/test_expand_format_string.c.pysam.c
create mode 100644 samtools/test/split/test_filter_header_rg.c
create mode 100644 samtools/test/split/test_filter_header_rg.c.pysam.c
create mode 100644 samtools/test/split/test_parse_args.c
create mode 100644 samtools/test/split/test_parse_args.c.pysam.c
copy samtools/test/{test.c.pysam.c => test.c} (95%)
create mode 100644 samtools/test/tview/test_get_rg_sample.c
create mode 100644 samtools/test/tview/test_get_rg_sample.c.pysam.c
create mode 100644 save/example.py
create mode 100644 save/pysam_bench.py
create mode 100755 save/pysam_test2.6.py
create mode 100644 save/pysam_test_stdin.py
create mode 100644 save/pysam_testpp.py
create mode 100755 save/segfault_tests.py
create mode 100644 save/vcf_test.py
create mode 100644 tests/AlignmentFile_test.py
create mode 100644 tests/SamFile_test.py
create mode 100644 tests/TestUtils.py
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