[med-svn] [sra-sdk] 02/06: Merge tag 'upstream/2.8.1+dfsg'

Andreas Tille tille at debian.org
Wed Jan 11 10:11:34 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 d52a3033d82cb9c795668f3d6af0e60927b656a6
Merge: 321e7d9 5eec480
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 11 07:20:53 2017 +0100

    Merge tag 'upstream/2.8.1+dfsg'
    
    Upstream version 2.8.1+dfsg

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 tools/bam-loader/bam-loader.c                      |  1270 +
 tools/bam-loader/bam-priv.h                        |   196 +
 tools/bam-loader/bam-reader.c                      |  1104 +
 tools/bam-loader/bam-reader.h                      |    98 +
 tools/bam-loader/bam.c                             |  4113 +++
 tools/bam-loader/bam.h                             |   597 +
 tools/bam-loader/config-file.cpp                   |   195 +
 tools/bam-loader/config-file.hpp                   |    65 +
 tools/bam-loader/fasta-file.cpp                    |   257 +
 tools/bam-loader/fasta-file.hpp                    |    63 +
 tools/bam-loader/hashtable.c                       |   878 +
 tools/bam-loader/hashtable.h                       |    55 +
 tools/bam-loader/loader-imp.c                      |  3130 ++
 tools/bam-loader/loader-imp.h                      |    30 +
 tools/bam-loader/low-match-count.cpp               |    72 +
 tools/bam-loader/low-match-count.h                 |    33 +
 tools/bam-loader/mate-distance-stats.cpp           |    23 +
 tools/bam-loader/mate-distance-stats.hpp           |    20 +
 tools/bam-loader/mem-bank.cpp                      |   477 +
 tools/bam-loader/mem-bank.h                        |    41 +
 tools/bam-loader/quality-quantizer.cpp             |   107 +
 tools/bam-loader/quality-quantizer.hpp             |    10 +
 tools/bam-loader/reference-writer.c                |   615 +
 tools/bam-loader/reference-writer.h                |    76 +
 tools/bam-loader/samview.c                         |   104 +
 tools/bam-loader/sequence-writer.c                 |   497 +
 tools/bam-loader/sequence-writer.h                 |    89 +
 tools/cache-mgr/Makefile                           |    76 +
 tools/cache-mgr/cache-mgr.c                        |  1415 +
 tools/ccextract/Makefile                           |    90 +
 tools/ccextract/ccextract.c                        |  1272 +
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 tools/cg-load/cg-load.c                            |  1270 +
 tools/cg-load/debug.h                              |    34 +
 tools/cg-load/defs.h                               |   163 +
 tools/cg-load/f1_3.c                               |    77 +
 tools/cg-load/f1_5.c                               |    78 +
 tools/cg-load/f1_7.c                               |    97 +
 tools/cg-load/f2_0.c                               |    98 +
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 tools/cg-load/f2_4.c                               |    33 +
 tools/cg-load/f2_5.c                               |    98 +
 tools/cg-load/factory-cmn.h                        |    57 +
 tools/cg-load/factory-evidence-dnbs.c              |   625 +
 tools/cg-load/factory-evidence-dnbs.h              |    46 +
 tools/cg-load/factory-evidence-intervals.c         |   396 +
 tools/cg-load/factory-evidence-intervals.h         |    46 +
 tools/cg-load/factory-file.h                       |    49 +
 tools/cg-load/factory-mappings.c                   |   539 +
 tools/cg-load/factory-mappings.h                   |    46 +
 tools/cg-load/factory-reads.c                      |   448 +
 tools/cg-load/factory-reads.h                      |    46 +
 tools/cg-load/factory-tag-lfr.c                    |   376 +
 tools/cg-load/factory-tag-lfr.h                    |    41 +
 tools/cg-load/file-version-factory.c               |   165 +
 tools/cg-load/file.c                               |   516 +
 tools/cg-load/file.h                               |   334 +
 tools/cg-load/formats.c                            |    54 +
 tools/cg-load/formats.h                            |    41 +
 tools/cg-load/writer-algn.c                        |   825 +
 tools/cg-load/writer-algn.h                        |    63 +
 tools/cg-load/writer-evidence-dnbs.c               |   246 +
 tools/cg-load/writer-evidence-dnbs.h               |    97 +
 tools/cg-load/writer-evidence-intervals.c          |   263 +
 tools/cg-load/writer-evidence-intervals.h          |    68 +
 tools/cg-load/writer-seq.c                         |   155 +
 tools/cg-load/writer-seq.h                         |    62 +
 tools/copycat/Makefile                             |   100 +
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 tools/copycat/ccbuffermgr.c                        |   234 +
 tools/copycat/ccbufferq.c                          |   175 +
 tools/copycat/cccat.c                              |  1797 ++
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 tools/copycat/ccfileformat.c                       |   405 +
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 tools/copycat/ccsra.c                              |  1239 +
 tools/copycat/ccsubchunk.c                         |   390 +
 tools/copycat/cctar.c                              |  2199 ++
 tools/copycat/cctree-dump.c                        |  1030 +
 tools/copycat/cctree-priv.h                        |   351 +
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 tools/copycat/copycat-priv.h                       |   229 +
 tools/copycat/copycat.c                            |  1251 +
 tools/copycat/debug.h                              |    75 +
 tools/copycat/magic                                | 18398 +++++++++++
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 tools/dbgap-mount/dbgap-mount-tool.c               |   561 +
 tools/dbgap-mount/dbgap-mount-tool.h               |    72 +
 tools/dbgap-mount/demo.c                           |   353 +
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 tools/fastdump/merge_sorter.h                      |    66 +
 tools/fastdump/raw_read_iter.c                     |   100 +
 tools/fastdump/raw_read_iter.h                     |    67 +
 tools/fastdump/readme.txt                          |    92 +
 tools/fastdump/sorter.c                            |   538 +
 tools/fastdump/sorter.h                            |    75 +
 tools/fastdump/special_iter.c                      |    98 +
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 tools/fastq-loader/common-writer.c                 |  1654 +
 tools/fastq-loader/common-writer.h                 |   164 +
 tools/fastq-loader/fastq-grammar.c                 |  2310 ++
 tools/fastq-loader/fastq-grammar.y                 |   478 +
 tools/fastq-loader/fastq-lex.c                     |  2888 ++
 tools/fastq-loader/fastq-lex.l                     |   256 +
 tools/fastq-loader/fastq-loader.c                  |   626 +
 tools/fastq-loader/fastq-parse.h                   |   169 +
 tools/fastq-loader/fastq-reader.c                  |   709 +
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 tools/fastq-loader/fastq-tokens.h                  |    67 +
 tools/fastq-loader/loader-imp.c                    |   256 +
 tools/fastq-loader/mmarray.c                       |   114 +
 tools/fastq-loader/parsing_rules.txt               |   106 +
 tools/fastq-loader/sequence-writer.c               |   366 +
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 tools/fuse/remote-cache.c                          |  2129 ++
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 tools/fuse/xml.c                                   |   516 +
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 tools/general-loader/gw-dumper.cpp                 |  1785 ++
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 tools/general-loader/utf8-like-int-codec.c         |   687 +
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 tools/kar/Makefile                                 |    99 +
 tools/kar/kar-args.c                               |   428 +
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 tools/kar/kar.c                                    |  2063 ++
 tools/kar/sra-kar.c                                |   431 +
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 tools/keyring-srv/keyring-data.c                   |   346 +
 tools/keyring-srv/keyring-data.h                   |   130 +
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 tools/sra-pileup/pileup_options.h                  |    62 +
 tools/sra-pileup/pileup_stat.c                     |   391 +
 tools/sra-pileup/pileup_stat.h                     |    40 +
 tools/sra-pileup/pileup_v2.c                       |   382 +
 tools/sra-pileup/pileup_v2.h                       |    40 +
 tools/sra-pileup/pileup_varcount.c                 |   139 +
 tools/sra-pileup/pileup_varcount.h                 |    40 +
 tools/sra-pileup/read_fkt.c                        |   718 +
 tools/sra-pileup/read_fkt.h                        |    82 +
 tools/sra-pileup/ref_regions.c                     |   825 +
 tools/sra-pileup/ref_regions.h                     |    71 +
 tools/sra-pileup/ref_walker.c                      |  1028 +
 tools/sra-pileup/ref_walker.h                      |   147 +
 tools/sra-pileup/ref_walker_0.c                    |   231 +
 tools/sra-pileup/ref_walker_0.h                    |   107 +
 tools/sra-pileup/report_deletes.c                  |   259 +
 tools/sra-pileup/report_deletes.h                  |    41 +
 tools/sra-pileup/reref.c                           |   550 +
 tools/sra-pileup/reref.h                           |    43 +
 tools/sra-pileup/rna_splice_log.c                  |   374 +
 tools/sra-pileup/rna_splice_log.h                  |    87 +
 tools/sra-pileup/sam-aligned.c                     |  2408 ++
 tools/sra-pileup/sam-aligned.h                     |    46 +
 tools/sra-pileup/sam-dump-opts.c                   |  1676 +
 tools/sra-pileup/sam-dump-opts.h                   |   306 +
 tools/sra-pileup/sam-dump.c                        |  4905 +++
 tools/sra-pileup/sam-dump3.c                       |   563 +
 tools/sra-pileup/sam-hdr.c                         |   728 +
 tools/sra-pileup/sam-hdr.h                         |    41 +
 tools/sra-pileup/sam-hdr1.c                        |   894 +
 tools/sra-pileup/sam-hdr1.h                        |    42 +
 tools/sra-pileup/sam-unaligned.c                   |  1565 +
 tools/sra-pileup/sam-unaligned.h                   |    44 +
 tools/sra-pileup/splitfastq.pl                     |    46 +
 tools/sra-pileup/sra-pileup.c                      |  1640 +
 tools/sra-pileup/walk_debug.c                      |   147 +
 tools/sra-pileup/walk_debug.h                      |    42 +
 tools/sra-pileup/writer.c                          |   137 +
 tools/sra-pileup/writer.h                          |    32 +
 tools/sra-seq-count/Makefile                       |    83 +
 tools/sra-seq-count/main_fkt.c                     |   203 +
 tools/sra-seq-count/options.h                      |    56 +
 tools/sra-seq-count/range.hpp                      |   307 +
 tools/sra-seq-count/sra-seq-count.cpp              |   688 +
 tools/sra-shell/Makefile                           |    58 +
 tools/sra-shell/guilib/Makefile                    |    71 +
 tools/sra-shell/job-exec/Makefile                  |    71 +
 tools/sra-shell/parser/Makefile                    |    71 +
 tools/sra-shell/parser/sra-shell-lex.l             |   103 +
 tools/sra-shell/parser/sra-shell.y                 |    54 +
 tools/sra-shell/sra-gui/Makefile                   |    80 +
 tools/sra-shell/sra-gui/sra-gui.c                  |    49 +
 tools/sra-shell/sra-shell/Makefile                 |    87 +
 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/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                            |   232 +
 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                            |    50 +
 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                                |   393 +
 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                      |   566 +
 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                              |  3724 +++
 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                     |   816 +
 tools/vdb-config/configure.h                       |    49 +
 tools/vdb-config/interactive.cpp                   |  1096 +
 tools/vdb-config/interactive.h                     |    50 +
 tools/vdb-config/util.cpp                          |  1084 +
 tools/vdb-config/util.hpp                          |   703 +
 tools/vdb-config/vdb-config-model.cpp              |   463 +
 tools/vdb-config/vdb-config-model.hpp              |   473 +
 tools/vdb-config/vdb-config.c                      |  1712 +
 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                         |   518 +
 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                          |  2351 ++
 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 ++
 2310 files changed, 313374 insertions(+), 299490 deletions(-)

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