[med-svn] [sra-sdk] 03/04: Merge tag 'upstream/2.8.1'
Andreas Tille
tille at debian.org
Tue Jan 10 15:30:14 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 075ea1d6a93481b61f8302f1b2e31f938535df10
Merge: 67dbdf6 06555f9
Author: Andreas Tille <tille at debian.org>
Date: Tue Jan 10 16:27:43 2017 +0100
Merge tag 'upstream/2.8.1'
Upstream version 2.8.1
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.../resources/htsjdk/samtools/cram/ce#5b.2.1.cram | Bin 0 -> 12668 bytes
.../resources/htsjdk/samtools/cram/ce#5b.3.0.cram | Bin 0 -> 2669 bytes
src/test/resources/htsjdk/samtools/cram/ce#5b.sam | 12 +
.../htsjdk/samtools/cram/ce#large_seq.2.1.cram | Bin 0 -> 101355 bytes
.../htsjdk/samtools/cram/ce#large_seq.3.0.cram | Bin 0 -> 84800 bytes
.../htsjdk/samtools/cram/ce#large_seq.sam | 3 +
.../htsjdk/samtools/cram/ce#supp.2.1.cram | Bin 0 -> 10649 bytes
.../htsjdk/samtools/cram/ce#supp.3.0.cram | Bin 0 -> 809 bytes
.../resources/htsjdk/samtools/cram/ce#supp.sam | 6 +
.../htsjdk/samtools/cram/ce#tag_depadded.2.1.cram | Bin 0 -> 11114 bytes
.../htsjdk/samtools/cram/ce#tag_depadded.3.0.cram | Bin 0 -> 1258 bytes
.../htsjdk/samtools/cram/ce#tag_depadded.sam | 11 +
.../htsjdk/samtools/cram/ce#tag_padded.2.1.cram | Bin 0 -> 10922 bytes
.../htsjdk/samtools/cram/ce#tag_padded.3.0.cram | Bin 0 -> 1082 bytes
.../htsjdk/samtools/cram/ce#tag_padded.sam | 11 +
.../htsjdk/samtools/cram/ce#unmap.2.1.cram | Bin 0 -> 10503 bytes
.../htsjdk/samtools/cram/ce#unmap.3.0.cram | Bin 0 -> 601 bytes
.../resources/htsjdk/samtools/cram/ce#unmap.sam | 6 +
.../htsjdk/samtools/cram/ce#unmap1.2.1.cram | Bin 0 -> 11730 bytes
.../htsjdk/samtools/cram/ce#unmap1.3.0.cram | Bin 0 -> 1505 bytes
.../resources/htsjdk/samtools/cram/ce#unmap1.sam | 20 +
.../htsjdk/samtools/cram/ce#unmap2.2.1.cram | Bin 0 -> 12587 bytes
.../htsjdk/samtools/cram/ce#unmap2.3.0.cram | Bin 0 -> 2404 bytes
.../resources/htsjdk/samtools/cram/ce#unmap2.sam | 29 +
src/test/resources/htsjdk/samtools/cram/ce.fa | 20803 +++++++++++++
src/test/resources/htsjdk/samtools/cram/ce.fa.fai | 7 +
.../htsjdk/samtools/cram/cramQueryTest.cram | Bin 0 -> 2863 bytes
.../htsjdk/samtools/cram/cramQueryTest.cram.bai | Bin 0 -> 336 bytes
.../htsjdk/samtools/cram/cramQueryTestEmpty.cram | Bin 0 -> 2183 bytes
.../samtools/cram/cramQueryTestEmpty.cram.bai | Bin 0 -> 48 bytes
.../htsjdk/samtools/cram/cramQueryWithBAI.cram | Bin 0 -> 8947 bytes
.../htsjdk/samtools/cram/cramQueryWithBAI.cram.bai | Bin 0 -> 152 bytes
.../htsjdk/samtools/cram/cramQueryWithCRAI.cram | Bin 0 -> 4131 bytes
.../samtools/cram/cramQueryWithCRAI.cram.crai | Bin 0 -> 59 bytes
.../resources/htsjdk/samtools/cram/fieldarith.sam | 15 +
.../samtools/cram/human_g1k_v37.20.21.1-100.dict | 3 +
.../samtools/cram/human_g1k_v37.20.21.1-100.fasta | 11 +
.../cram/human_g1k_v37.20.21.1-100.fasta.fai | 2 +
.../cram/human_g1k_v37.20.21.10M-10M200k.dict | 3 +
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta | 5002 +++
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai | 2 +
.../htsjdk/samtools/cram/io/bzip2-test.bz2 | Bin 0 -> 56 bytes
src/test/resources/htsjdk/samtools/cram/test.cram | Bin 0 -> 3433 bytes
.../resources/htsjdk/samtools/cram/test.cram.bai | Bin 0 -> 96 bytes
src/test/resources/htsjdk/samtools/cram/test.dict | 2 +
src/test/resources/htsjdk/samtools/cram/test.fa | 2 +
.../resources/htsjdk/samtools/cram/test.fa.fai | 1 +
src/test/resources/htsjdk/samtools/cram/test2.cram | Bin 0 -> 3433 bytes
src/test/resources/htsjdk/samtools/cram/test2.dict | 2 +
src/test/resources/htsjdk/samtools/cram/test2.fa | 2 +
.../resources/htsjdk/samtools/cram/test2.fa.fai | 1 +
.../htsjdk/samtools/cram/xx#blank.2.1.cram | Bin 0 -> 10080 bytes
.../htsjdk/samtools/cram/xx#blank.3.0.cram | Bin 0 -> 140 bytes
.../resources/htsjdk/samtools/cram/xx#blank.sam | 0
.../htsjdk/samtools/cram/xx#large_aux.2.1.cram | Bin 0 -> 35824 bytes
.../htsjdk/samtools/cram/xx#large_aux.3.0.cram | Bin 0 -> 20418 bytes
.../htsjdk/samtools/cram/xx#large_aux.sam | 4 +
.../htsjdk/samtools/cram/xx#large_aux2.2.1.cram | Bin 0 -> 10868 bytes
.../htsjdk/samtools/cram/xx#large_aux2.3.0.cram | Bin 0 -> 1008 bytes
.../htsjdk/samtools/cram/xx#large_aux2.sam | 11 +
.../htsjdk/samtools/cram/xx#minimal.2.1.cram | Bin 0 -> 10995 bytes
.../htsjdk/samtools/cram/xx#minimal.3.0.cram | Bin 0 -> 1096 bytes
.../resources/htsjdk/samtools/cram/xx#minimal.sam | 10 +
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.../htsjdk/samtools/cram/xx#pair.3.0.cram | Bin 0 -> 590 bytes
.../resources/htsjdk/samtools/cram/xx#pair.sam | 7 +
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.../resources/htsjdk/samtools/cram/xx#rg.3.0.cram | Bin 0 -> 794 bytes
src/test/resources/htsjdk/samtools/cram/xx#rg.sam | 13 +
.../htsjdk/samtools/cram/xx#tlen.2.1.cram | Bin 0 -> 11312 bytes
.../htsjdk/samtools/cram/xx#tlen.3.0.cram | Bin 0 -> 1296 bytes
.../htsjdk/samtools/cram/xx#tlen2.2.1.cram | Bin 0 -> 11380 bytes
.../htsjdk/samtools/cram/xx#tlen2.3.0.cram | Bin 0 -> 1359 bytes
.../htsjdk/samtools/cram/xx#triplet.2.1.cram | Bin 0 -> 10853 bytes
.../htsjdk/samtools/cram/xx#triplet.3.0.cram | Bin 0 -> 950 bytes
.../resources/htsjdk/samtools/cram/xx#triplet.sam | 7 +
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.../htsjdk/samtools/cram/xx#unsorted.3.0.cram | Bin 0 -> 1262 bytes
.../resources/htsjdk/samtools/cram/xx#unsorted.sam | 8 +
src/test/resources/htsjdk/samtools/cram/xx.fa | 5 +
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.../htsjdk/samtools/cram_query_sorted.cram | Bin 0 -> 13266 bytes
.../htsjdk/samtools/cram_query_sorted.fasta | 40 +
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src/test/resources/htsjdk/samtools/cram_tlen.fasta | 41 +
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.../htsjdk/samtools/cram_with_crai_index.cram | Bin 0 -> 4213 bytes
.../htsjdk/samtools/cram_with_crai_index.cram.crai | Bin 0 -> 77 bytes
src/test/resources/htsjdk/samtools/empty.bai | Bin 0 -> 8 bytes
src/test/resources/htsjdk/samtools/empty.bam | Bin 0 -> 90 bytes
.../htsjdk/samtools/empty_no_empty_gzip_block.bai | Bin 0 -> 8 bytes
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src/test/resources/htsjdk/samtools/hg19mini.dict | 5 +
src/test/resources/htsjdk/samtools/hg19mini.fasta | 804 +
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.../intervallist/IntervalListFromVCFTest.vcf | 53 +
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.../IntervalListchr123_empty.interval_list | 4 +
src/test/resources/htsjdk/samtools/inttest.bam | Bin 0 -> 329 bytes
src/test/resources/htsjdk/samtools/inttest.sam | 26 +
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src/test/resources/htsjdk/samtools/issue76.bam | Bin 0 -> 5121 bytes
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.../htsjdk/samtools/liftover/hg18ToHg19.over.chain | 30850 +++++++++++++++++++
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.../reference/Homo_sapiens_assembly18.trimmed.dict | 3 +
.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ++++++++++
.../Homo_sapiens_assembly18.trimmed.fasta.fai | 2 +
.../Homo_sapiens_assembly18.trimmed.nodict.fasta | 16946 ++++++++++
...omo_sapiens_assembly18.trimmed.nodict.fasta.fai | 2 +
.../Homo_sapiens_assembly18.trimmed.noindex.fasta | 16946 ++++++++++
.../reference_with_trailing_whitespace.dict | 3 +
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src/test/resources/htsjdk/samtools/roundtrip.sam | 16 +
src/test/resources/htsjdk/samtools/samFilter01.js | 2 +
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src/test/resources/htsjdk/samtools/unsorted.sam | 15 +
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src/test/resources/htsjdk/tribble/Tb.vcf.idx | Bin 0 -> 998966 bytes
src/test/resources/htsjdk/tribble/basicDbSNP.dbsnp | 43 +
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src/test/resources/htsjdk/tribble/gwas/smallp.gwas | 20 +
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src/test/resources/htsjdk/tribble/large.txt | 165 +
src/test/resources/htsjdk/tribble/sites.bed | 1000 +
src/test/resources/htsjdk/tribble/soapsnp.txt | 24 +
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src/test/resources/htsjdk/tribble/test.bed | 9 +
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src/test/resources/htsjdk/tribble/test.vcf | 24 +
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src/test/resources/htsjdk/tribble/testGeliText.txt | 50 +
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src/test/resources/htsjdk/tribble/trio.vcf | 100 +
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src/test/resources/htsjdk/tribble/trioDup.vcf | 75 +
src/test/resources/htsjdk/tribble/vcfexample.vcf | 12 +
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src/test/resources/htsjdk/variant/HiSeq.10000.vcf | 10001 ++++++
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src/test/resources/htsjdk/variant/breakpoint.vcf | 6 +
.../htsjdk/variant/dbsnp_135.b37.1000.vcf | 249 +
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src/test/resources/htsjdk/variant/ex2.vcf | 23 +
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.../htsjdk/variant/structuralvariants.vcf | 22 +
.../Homo_sapiens_assembly18.trimmed.dict | 3 +
.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ++++++++++
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tools/sra-shell/sra-shell/sra-shell.c | 49 -
tools/sra-shell/turboVision/Makefile | 71 -
tools/sra-sort/Makefile | 125 -
tools/sra-sort/Makefile.cc | 24 -
tools/sra-sort/Makefile.clang | 27 -
tools/sra-sort/Makefile.gcc | 27 -
tools/sra-sort/Makefile.vc++ | 24 -
tools/sra-sort/buff-writer.c | 789 -
tools/sra-sort/buff-writer.h | 64 -
tools/sra-sort/caps.c | 125 -
tools/sra-sort/caps.h | 70 -
tools/sra-sort/capture-first-half-aligned.c | 192 -
tools/sra-sort/col-pair.c | 818 -
tools/sra-sort/col-pair.h | 323 -
tools/sra-sort/csra-pair.c | 228 -
tools/sra-sort/csra-pair.h | 87 -
tools/sra-sort/csra-tbl.c | 798 -
tools/sra-sort/csra-tbl.h | 83 -
tools/sra-sort/ctx.h | 109 -
tools/sra-sort/db-pair.c | 885 -
tools/sra-sort/db-pair.h | 208 -
tools/sra-sort/dir-pair.c | 504 -
tools/sra-sort/dir-pair.h | 124 -
tools/sra-sort/dump-blob-boundaries.c | 203 -
tools/sra-sort/except.c | 231 -
tools/sra-sort/except.h | 160 -
tools/sra-sort/gcc-ped.sh | 39 -
tools/sra-sort/glob-poslen.c | 349 -
tools/sra-sort/glob-poslen.h | 95 -
tools/sra-sort/id-mapper-col.c | 260 -
tools/sra-sort/id-mapper-col.h | 55 -
tools/sra-sort/idx-mapping.c | 88 -
tools/sra-sort/idx-mapping.h | 59 -
tools/sra-sort/map-file.c | 1192 -
tools/sra-sort/map-file.h | 172 -
tools/sra-sort/mapping-row-set.c | 496 -
tools/sra-sort/mem.c | 68 -
tools/sra-sort/mem.h | 128 -
tools/sra-sort/membank-priv.h | 44 -
tools/sra-sort/membank.c | 296 -
tools/sra-sort/meta-pair.c | 458 -
tools/sra-sort/meta-pair.h | 109 -
tools/sra-sort/paged-membank.c | 244 -
tools/sra-sort/paged-mmapbank.c | 399 -
tools/sra-sort/poslen-col-pair.c | 559 -
tools/sra-sort/poslen-col-pair.h | 63 -
tools/sra-sort/ref-alignid-col.c | 702 -
tools/sra-sort/ref-alignid-col.h | 53 -
tools/sra-sort/row-set-priv.h | 44 -
tools/sra-sort/row-set.c | 208 -
tools/sra-sort/row-set.h | 215 -
tools/sra-sort/run.c | 388 -
tools/sra-sort/simple-row-set.c | 212 -
tools/sra-sort/sort-defs.h | 109 -
tools/sra-sort/sorting-row-set.c | 405 -
tools/sra-sort/sra-sort.c | 746 -
tools/sra-sort/sra-sort.h | 171 -
tools/sra-sort/status.h | 48 -
tools/sra-sort/tbl-pair.c | 1055 -
tools/sra-sort/tbl-pair.h | 209 -
tools/sra-sort/xcheck-ref-align.c | 411 -
tools/sra-sort/xcheck.h | 49 -
tools/sra-stat/Makefile | 80 -
tools/sra-stat/sra-stat.c | 3634 ---
tools/sra-stat/sra-stat.h | 42 -
tools/sra-stat/sra.c | 446 -
tools/sra/.cvsignore | 1 -
tools/sra/Makefile | 77 -
tools/sra/sra-dbcc.c | 435 -
tools/sra/table-vers.c | 232 -
tools/srapath/Makefile | 79 -
tools/srapath/cgi_request.c | 853 -
tools/srapath/cgi_request.h | 129 -
tools/srapath/helper.c | 464 -
tools/srapath/helper.h | 108 -
tools/srapath/line_iter.c | 241 -
tools/srapath/line_iter.h | 71 -
tools/srapath/srapath.c | 439 -
tools/update-schema/.cvsignore | 1 -
tools/update-schema/Makefile | 77 -
tools/update-schema/update-schema.c | 454 -
tools/util/Makefile | 392 -
tools/util/crc32sum.c | 272 -
tools/util/kdb-index.c | 257 -
tools/util/kdbmeta.c | 1332 -
tools/util/mac/syspass.c | 48 -
tools/util/md5cp.c | 702 -
tools/util/pacbio-correct.c | 208 -
tools/util/pseudo-aligner.cpp | 515 -
tools/util/rcexplain.c | 127 -
tools/util/rowwritetest.c | 433 -
tools/util/samview.c | 80 -
tools/util/schema-replace.c | 379 -
tools/util/sortreadtest.c | 351 -
tools/util/syspass-priv.h | 44 -
tools/util/test-sra-priv.h | 46 -
tools/util/test-sra.c | 3380 --
tools/util/testld.c | 249 -
tools/util/txt2kdb.c | 579 -
tools/util/unix/PrintOS.c | 66 -
tools/util/unix/syspass.c | 62 -
tools/util/vdb-lock.c | 154 -
tools/util/vdb-passwd.c | 307 -
tools/util/vdb-unlock.c | 156 -
tools/util/win/PrintOS.c | 60 -
tools/util/win/syspass.c | 53 -
tools/vcf-loader/.gitignore | 1 -
tools/vcf-loader/Makefile | 128 -
tools/vcf-loader/vcf-database.c | 168 -
tools/vcf-loader/vcf-database.h | 40 -
tools/vcf-loader/vcf-grammar.c | 1686 -
tools/vcf-loader/vcf-grammar.h | 61 -
tools/vcf-loader/vcf-grammar.y | 123 -
tools/vcf-loader/vcf-lex.c | 2528 --
tools/vcf-loader/vcf-lex.l | 132 -
tools/vcf-loader/vcf-loader.c | 124 -
tools/vcf-loader/vcf-parse.h | 89 -
tools/vcf-loader/vcf-reader.c | 438 -
tools/vcf-loader/vcf-reader.h | 110 -
tools/vdb-config/Makefile | 82 -
tools/vdb-config/configure.cpp | 815 -
tools/vdb-config/configure.h | 49 -
tools/vdb-config/interactive.cpp | 1084 -
tools/vdb-config/interactive.h | 50 -
tools/vdb-config/util.cpp | 1125 -
tools/vdb-config/util.hpp | 702 -
tools/vdb-config/vdb-config-model.cpp | 440 -
tools/vdb-config/vdb-config-model.hpp | 482 -
tools/vdb-config/vdb-config.c | 1740 --
tools/vdb-config/vdb-config2.cpp | 30 -
tools/vdb-config/vdb-config2.h | 29 -
tools/vdb-copy/.gitignore | 17 -
tools/vdb-copy/Makefile | 91 -
tools/vdb-copy/coldefs.c | 775 -
tools/vdb-copy/coldefs.h | 250 -
tools/vdb-copy/column_match.c | 31 -
tools/vdb-copy/column_match.h | 42 -
tools/vdb-copy/config_values.c | 54 -
tools/vdb-copy/config_values.h | 49 -
tools/vdb-copy/context.c | 473 -
tools/vdb-copy/context.h | 183 -
tools/vdb-copy/copy_context.c | 47 -
tools/vdb-copy/copy_context.h | 58 -
tools/vdb-copy/copy_meta.c | 517 -
tools/vdb-copy/copy_meta.h | 46 -
tools/vdb-copy/definitions.h | 112 -
tools/vdb-copy/get_platform.c | 168 -
tools/vdb-copy/get_platform.h | 46 -
tools/vdb-copy/helper.c | 919 -
tools/vdb-copy/helper.h | 225 -
tools/vdb-copy/matcher_input.h | 55 -
tools/vdb-copy/namelist_tools.c | 187 -
tools/vdb-copy/namelist_tools.h | 52 -
tools/vdb-copy/num-gen.c | 848 -
tools/vdb-copy/num-gen.h | 225 -
tools/vdb-copy/redactval.c | 230 -
tools/vdb-copy/redactval.h | 120 -
tools/vdb-copy/type_matcher.c | 850 -
tools/vdb-copy/type_matcher.h | 71 -
tools/vdb-copy/vdb-copy-includes.h | 121 -
tools/vdb-copy/vdb-copy.c | 1456 -
tools/vdb-copy/vdb-copy.kfg | 94 -
tools/vdb-decrypt/Makefile | 102 -
tools/vdb-decrypt/shared.c | 1271 -
tools/vdb-decrypt/shared.h | 93 -
tools/vdb-decrypt/vdb-decrypt.c | 269 -
tools/vdb-decrypt/vdb-encrypt.c | 215 -
tools/vdb-diff/Makefile | 79 -
tools/vdb-diff/coldefs.c | 211 -
tools/vdb-diff/coldefs.h | 105 -
tools/vdb-diff/namelist_tools.c | 299 -
tools/vdb-diff/namelist_tools.h | 59 -
tools/vdb-diff/vdb-diff.c | 1002 -
tools/vdb-dump/.gitignore | 2 -
tools/vdb-dump/Makefile | 92 -
tools/vdb-dump/help.txt | 352 -
tools/vdb-dump/vdb-boot.c | 448 -
tools/vdb-dump/vdb-boot.vschema | 52 -
tools/vdb-dump/vdb-dump-bin.c | 1496 -
tools/vdb-dump/vdb-dump-bin.h | 46 -
tools/vdb-dump/vdb-dump-coldefs.c | 846 -
tools/vdb-dump/vdb-dump-coldefs.h | 110 -
tools/vdb-dump/vdb-dump-context.c | 649 -
tools/vdb-dump/vdb-dump-context.h | 220 -
tools/vdb-dump/vdb-dump-fastq.c | 1132 -
tools/vdb-dump/vdb-dump-fastq.h | 47 -
tools/vdb-dump/vdb-dump-filter.c | 116 -
tools/vdb-dump/vdb-dump-filter.h | 82 -
tools/vdb-dump/vdb-dump-formats.c | 383 -
tools/vdb-dump/vdb-dump-formats.h | 51 -
tools/vdb-dump/vdb-dump-helper.c | 772 -
tools/vdb-dump/vdb-dump-helper.h | 107 -
tools/vdb-dump/vdb-dump-interact.c | 265 -
tools/vdb-dump/vdb-dump-interact.h | 50 -
tools/vdb-dump/vdb-dump-print.c | 1349 -
tools/vdb-dump/vdb-dump-print.h | 86 -
tools/vdb-dump/vdb-dump-redir.c | 120 -
tools/vdb-dump/vdb-dump-redir.h | 64 -
tools/vdb-dump/vdb-dump-repo.c | 281 -
tools/vdb-dump/vdb-dump-repo.h | 46 -
tools/vdb-dump/vdb-dump-row-context.h | 71 -
tools/vdb-dump/vdb-dump-str.c | 540 -
tools/vdb-dump/vdb-dump-str.h | 100 -
tools/vdb-dump/vdb-dump-tools.c | 528 -
tools/vdb-dump/vdb-dump-tools.h | 60 -
tools/vdb-dump/vdb-dump.c | 2335 --
tools/vdb-dump/vdb_info.c | 1528 -
tools/vdb-dump/vdb_info.h | 47 -
tools/vdb-validate/Makefile | 96 -
tools/vdb-validate/check-corrupt.cpp | 764 -
tools/vdb-validate/vdb-validate.c | 3351 --
2496 files changed, 299503 insertions(+), 326672 deletions(-)
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