Run of fresh-snapshots for htslib

Try this locally (using silver-platter):

debian-svp new-upstream --snapshot htslib 
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Processing: htslib
Total 10508 (delta 7450), reused 10315 (delta 7265)
Total 82 (delta 17), reused 79 (delta 14)

Total 0 (delta 0), reused 0 (delta 0)
Using upstream branch https://github.com/samtools/htslib (guessed)
Total 2866 (delta 1004), reused 1024 (delta 992), pack-reused 1823

Using version string 1.9+git20190906.a44f5ae.
Exporting upstream branch revision b'git-v1:a44f5ae0b8776ca05d3bc895a9ba7fe3ab6272a6' to create the tarball
Total 2866 (delta 1004), reused 1024 (delta 992), pack-reused 1823

/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.8 points at non-present sha bdceda980eac4161d85f69a6037c27913a6ebd01
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.9 points at non-present sha e3256fe287f0e28c8b512d9213e126fc653fcba5
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.7 points at non-present sha 914227859d23dddbfee18a5b3ced6125a2e6a478
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.6 points at non-present sha 233c9dcfb74cb48d45fe59b9b4f2c2b9a43e62b9
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.8 points at non-present sha bdceda980eac4161d85f69a6037c27913a6ebd01
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.9 points at non-present sha e3256fe287f0e28c8b512d9213e126fc653fcba5
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.7 points at non-present sha 914227859d23dddbfee18a5b3ced6125a2e6a478
  UserWarning)
/usr/lib/python3/dist-packages/dulwich/repo.py:415: UserWarning: ref refs/tags/1.6 points at non-present sha 233c9dcfb74cb48d45fe59b9b4f2c2b9a43e62b9
  UserWarning)
1.8 does not point to a valid object
1.9 does not point to a valid object
1.7 does not point to a valid object
1.6 does not point to a valid object
All changes applied successfully.
1.8 does not point to a valid object
1.9 does not point to a valid object
1.7 does not point to a valid object
1.6 does not point to a valid object
Committing to: /home/janitor/tmp/tmpkla7b8qt/htslib/
added .appveyor.yml
added .gitattributes
added .gitignore
added .travis.yml
modified LICENSE
modified Makefile
modified NEWS
added README.md
added aclocal.m4
modified bcf_sr_sort.c
modified bcf_sr_sort.h
modified bgzf.c
modified bgzip.c
modified config.mk.in
modified configure.ac
modified cram/cram.h
modified cram/cram_codecs.c
modified cram/cram_codecs.h
modified cram/cram_decode.c
modified cram/cram_decode.h
modified cram/cram_encode.c
modified cram/cram_encode.h
modified cram/cram_external.c
modified cram/cram_index.c
modified cram/cram_index.h
modified cram/cram_io.c
modified cram/cram_io.h
modified cram/cram_samtools.c
modified cram/cram_samtools.h
modified cram/cram_stats.c
modified cram/cram_stats.h
modified cram/cram_structs.h
deleted cram/files.c
modified cram/mFILE.c
modified cram/mFILE.h
modified cram/misc.h
modified cram/open_trace_file.c
modified cram/open_trace_file.h
modified cram/os.h
modified cram/pooled_alloc.h
modified cram/rANS_byte.h
modified cram/rANS_static.c
deleted cram/sam_header.c
deleted cram/sam_header.h
modified cram/string_alloc.c
modified cram/string_alloc.h
modified debian/changelog
modified errmod.c
modified faidx.c
added header.c
added header.h
modified hfile.c
modified hfile_internal.h
modified hfile_libcurl.c
modified hfile_s3.c
added hfile_s3_write.c
modified hts.c
modified hts_internal.h
modified htsfile.1
modified htsfile.c
modified htslib/bgzf.h
modified htslib/cram.h
modified htslib/faidx.h
modified htslib/hfile.h
modified htslib/hts.h
modified htslib/hts_log.h
modified htslib/hts_os.h
modified htslib/kbitset.h
modified htslib/khash.h
modified htslib/kseq.h
modified htslib/ksort.h
modified htslib/kstring.h
modified htslib/sam.h
modified htslib/synced_bcf_reader.h
modified htslib/tbx.h
modified htslib/thread_pool.h
modified htslib/vcf.h
modified htslib/vcfutils.h
added htslib-s3-plugin.7
modified htslib.mk
modified htslib_vars.mk
modified knetfile.c
modified kstring.c
modified m4/hts_prog_cc_warnings.m4
modified probaln.c
modified realn.c
modified regidx.c
added region.c
modified sam.c
added sam_internal.h
modified synced_bcf_reader.c
modified tabix.1
modified tabix.c
modified tbx.c
added test/colons.bam
added test/colons.bam.bai
modified test/compare_sam.pl
modified test/cross_validate.sh
added test/emptyfile
modified test/fieldarith.c
added test/fuzz
added test/fuzz/hts_open_fuzzer.c
modified test/hfile.c
added test/index.bam.bai
added test/index.bam.csi
added test/index.bcf.csi
added test/index.cram.crai
added test/index.sam
added test/index.sam.gz.bai
added test/index.sam.gz.csi
added test/index.vcf
added test/index.vcf.gz.csi
added test/index.vcf.gz.tbi
added test/maintainer
added test/maintainer/check_copyright.pl
added test/maintainer/check_spaces.pl
added test/mpileup
added test/mpileup/c1#pad1.out
added test/mpileup/c1#pad1.sam
added test/mpileup/c1#pad2.out
added test/mpileup/c1#pad2.sam
added test/mpileup/c1#pad3.out
added test/mpileup/c1#pad3.sam
added test/mpileup/mp_D.out
added test/mpileup/mp_D.sam
added test/mpileup/mp_DI.out
added test/mpileup/mp_DI.sam
added test/mpileup/mp_I.out
added test/mpileup/mp_I.sam
added test/mpileup/mp_ID.out
added test/mpileup/mp_ID.sam
added test/mpileup/mp_N.out
added test/mpileup/mp_N.sam
added test/mpileup/mp_N2.out
added test/mpileup/mp_N2.sam
added test/mpileup/mp_P.out
added test/mpileup/mp_P.sam
added test/mpileup/mpileup.tst
added test/mpileup/small.bam
added test/mpileup/small.out
added test/mpileup/test-pileup.sh
added test/no_hdr_sq_1.bam
added test/no_hdr_sq_1.bam.csi
added test/no_hdr_sq_1.expected.sam
added test/pileup.c
modified test/sam.c
added test/simple_test_driver.sh
modified test/tabix/test-tabix.sh
added test/tabix.out
modified test/test-bcf-sr.pl
modified test/test-bcf-translate.c
added test/test-parse-reg.c
modified test/test-vcf-api.c
modified test/test-vcf-api.out
modified test/test.pl
modified test/test_bgzf.c
added test/test_index.c
added test/test_kstring.c
modified test/test_realn.c
modified test/test_view.c
added test/thrash_threads7.c
added test/xx#MD.sam
added test/xx#MD2.sam
modified test/xx#blank.sam
modified test/xx.fa
modified test/xx.fa.fai
modified textutils.c
modified textutils_internal.h
modified thread_pool.c
modified thread_pool_internal.h
modified vcf.c
modified vcf_sweep.c
modified vcfutils.c
modified version.sh
Committed revision 496.
Worker failed: An error occurred refreshing quilt patch testShebang.patch: 

Applying patch debian/patches/testShebang.patch
patching file test/test-bcf-sr.pl
Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- rejects in file test/test-bcf-sr.pl
patching file test/test-logging.pl
patching file test/test.pl
Patch debian/patches/testShebang.patch does not apply (enforce with -f)

Elapsed time: 0:05:00.294114

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