[med-svn] [sra-sdk] 02/04: Merge tag 'upstream/2.5.7'

Andreas Tille tille at debian.org
Wed Dec 30 07:52:54 UTC 2015


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sra-sdk.

commit e272747906d949ef36d475ed303cfe78205a032a
Merge: 9df1a87 82d7c33
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 30 08:41:17 2015 +0100

    Merge tag 'upstream/2.5.7'
    
    Upstream version 2.5.7

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 tools/kar/sra-kar.vers                             |    2 +-
 tools/kar/sra-kar.vers.h                           |    2 +-
 tools/keyring-srv/keyring-data.c                   |    8 +-
 tools/keyring-srv/keyring-srv.vers                 |    2 +-
 tools/{sra-dbcc => kget}/Makefile                  |   31 +-
 tools/kget/kget.c                                  |  688 +++
 tools/kget/kget.vers                               |    1 +
 tools/kqsh/kqsh.c                                  |    2 +-
 tools/kqsh/kqsh.vers                               |    2 +-
 tools/meta-sync/meta-sync.c                        | 1517 ------
 tools/meta-sync/meta-sync.pl                       |   41 -
 tools/meta-sync/meta-sync.vers                     |    1 -
 tools/nenctool/nenctest.c                          |   10 +-
 tools/nenctool/nenctest.vers                       |    2 +-
 tools/nenctool/nenctool.c                          |   12 +-
 tools/nenctool/nenctool.vers                       |    2 +-
 tools/nencvalid/nencvalid.c                        |    9 +-
 tools/nencvalid/nencvalid.vers                     |    2 +-
 tools/{fix-run-stat => ngs-pileup}/Makefile        |   46 +-
 tools/ngs-pileup/main.cpp                          |  164 +
 tools/ngs-pileup/ngs-pileup.cpp                    |  206 +
 tools/ngs-pileup/ngs-pileup.hpp                    |   97 +
 tools/ngs-pileup/ngs-pileup.vers                   |    1 +
 tools/ngs-pileup/ngs-pileup.vers.h                 |    1 +
 tools/pacbio-load/Makefile                         |    8 +-
 tools/pacbio-load/pacbio-load.vers                 |    2 +-
 tools/pacbio-load/pl-consensus.c                   |  227 +-
 tools/pacbio-load/pl-context.c                     |    4 +-
 tools/pacbio-load/pl-regions.c                     |    4 +-
 tools/pacbio-load/pl-tools.c                       |   22 +-
 tools/{deseq => pileup-stats}/Makefile             |   47 +-
 tools/pileup-stats/pileup-stats.cpp                |  719 +++
 tools/pileup-stats/pileup-stats.vers               |    1 +
 tools/pore-load/GeneralWriter.py                   |  312 ++
 tools/pore-load/README.md                          |   10 +
 tools/pore-load/pore-load.py                       |  406 ++
 tools/prefetch/Makefile                            |    3 +-
 tools/prefetch/kfile-no-q.c                        |  215 +
 .../loader-imp3.h => prefetch/kfile-no-q.h}        |   26 +-
 tools/prefetch/prefetch.c                          | 1020 +++-
 tools/prefetch/prefetch.vers                       |    2 +-
 tools/prefetch/prefetch.vers.h                     |    2 +-
 tools/qual-recal/Makefile                          |  101 -
 tools/qual-recal/make_histo_data.sh                |   12 -
 tools/qual-recal/qual-recal.c                      |  654 ---
 tools/qual-recalib-stat/Makefile                   |    2 -
 tools/qual-recalib-stat/context.c                  |    6 +-
 tools/qual-recalib-stat/context.h                  |    4 +-
 tools/qual-recalib-stat/num-gen.c                  |  848 ----
 tools/qual-recalib-stat/num-gen.h                  |  225 -
 tools/qual-recalib-stat/progressbar.c              |  182 -
 tools/qual-recalib-stat/progressbar.h              |   75 -
 tools/qual-recalib-stat/qual-recalib-stat.c        |   39 +-
 tools/qual-recalib-stat/qual-recalib-stat.vers     |    2 +-
 tools/qual-recalib-stat/qual-recalib-stat.vers.h   |    2 +-
 tools/qual-recalib-stat/ref_exclude.c              |    8 +-
 tools/qual-recalib-stat/stat_mod.c                 |    4 +-
 tools/qual-recalib-stat/stat_mod_1.c               |    4 +-
 tools/qual-recalib-stat/stat_mod_2.c               |    4 +-
 tools/qual-recalib-stat/writer.c                   |   58 +-
 tools/qual-recalib-stat/writer.h                   |    1 -
 tools/rd-filter-redact/rd-filter-redact.c          |    6 +-
 tools/rd-filter-redact/rd-filter-redact.vers       |    2 +-
 tools/rd-filter-redact/read-filter-redact.c        |    6 +-
 tools/rd-filter-redact/read-filter-redact.vers     |    2 +-
 tools/rd-filter-redact/read-filter-redact.vers.h   |    2 +-
 tools/rd-filter-redact/test-read-write-cursor.vers |    2 +-
 tools/{check-blob-size => ref-variation}/Makefile  |   73 +-
 tools/ref-variation/common.cpp                     |   70 +
 .../vdb_info.h => ref-variation/common.h}          |   31 +-
 tools/ref-variation/helper.cpp                     | 1404 ++++++
 tools/ref-variation/helper.h                       |  605 +++
 tools/ref-variation/ref-variation.cpp              | 2102 +++++++++
 tools/ref-variation/ref-variation.vers             |    1 +
 tools/ref-variation/ref-variation.vers.h           |    1 +
 tools/ref-variation/var-expand.cpp                 |  448 ++
 tools/ref-variation/var-expand.vers                |    1 +
 tools/ref-variation/var-expand.vers.h              |    1 +
 tools/refseq-load/refseq-load.vers                 |    1 +
 tools/run-stat/.gitignore                          |    6 -
 tools/run-stat/Makefile                            |  120 -
 tools/run-stat/chart.c                             |  465 --
 tools/run-stat/chart.h                             |  109 -
 tools/run-stat/context.c                           |  439 --
 tools/run-stat/context.h                           |   98 -
 tools/run-stat/helper.c                            |  715 ---
 tools/run-stat/helper.h                            |  126 -
 tools/run-stat/key_value.c                         |  549 ---
 tools/run-stat/mod_cmn.c                           |  329 --
 tools/run-stat/mod_cmn.h                           |  149 -
 tools/run-stat/mod_reads.c                         |  747 ---
 tools/run-stat/mod_reads_defs.h                    |  128 -
 tools/run-stat/mod_reads_helper.c                  |  575 ---
 tools/run-stat/mod_reads_helper.h                  |   61 -
 tools/run-stat/num-gen.c                           |  497 --
 tools/run-stat/progressbar.c                       |  191 -
 tools/run-stat/progressbar.h                       |   76 -
 tools/run-stat/rd_filter.c                         |  243 -
 tools/run-stat/rd_filter.h                         |   98 -
 tools/run-stat/run-stat.c                          |  703 ---
 tools/run-stat/run-stat.vers                       |    1 -
 tools/run-stat/svg.c                               |  753 ---
 tools/run-stat/svg.h                               |  117 -
 tools/sam-dump/debug.h                             |   34 -
 tools/sam-dump/sam-dump.c                          | 4870 --------------------
 tools/sam-dump/sam-dump.vers                       |    1 -
 tools/sra-dbcc/sra-dbcc.c                          | 1577 -------
 tools/sra-dbcc/sra-dbcc.vers                       |    1 -
 tools/sra-dump/abi-dump.vers                       |    2 +-
 tools/sra-dump/abi-dump.vers.h                     |    2 +-
 tools/sra-dump/abi.c                               |    4 +-
 tools/sra-dump/core.c                              |    9 +-
 tools/sra-dump/factory.c                           |    4 +-
 tools/sra-dump/fasta_dump.c                        |    6 +-
 tools/sra-dump/fastq-dump.vers                     |    2 +-
 tools/sra-dump/fastq-dump.vers.h                   |    2 +-
 tools/sra-dump/fastq.c                             |    4 +-
 tools/sra-dump/illumina-dump.vers                  |    2 +-
 tools/sra-dump/illumina-dump.vers.h                |    2 +-
 tools/sra-dump/sff-dump.vers                       |    2 +-
 tools/sra-dump/sff-dump.vers.h                     |    2 +-
 tools/sra-dump/sra-dump.c                          |   20 +-
 tools/sra-dump/sra-dump.vers                       |    2 +-
 tools/sra-load/Makefile                            |   19 +-
 tools/sra-load/abi-load.vers                       |    2 +-
 tools/sra-load/common-xml.c                        |   11 +-
 tools/sra-load/experiment-xml.c                    |    6 +-
 tools/sra-load/fastq-load.vers                     |    2 +-
 tools/sra-load/helicos-load.vers                   |    2 +-
 tools/sra-load/illumina-load.vers                  |    2 +-
 tools/sra-load/loader.c                            |   28 +-
 tools/sra-load/pacbio-loadxml.vers                 |    2 +-
 tools/sra-load/sff-load.vers                       |    2 +-
 tools/sra-load/srf-absolid.c                       |   15 +-
 tools/sra-load/srf-load.vers                       |    2 +-
 tools/sra-load/writer-illumina.c                   |    2 +-
 tools/sra-load/ztr-huffman.c                       |   15 +-
 tools/sra-pileup/Makefile                          |   27 +-
 tools/sra-pileup/cg_tools.c                        |    2 +-
 tools/sra-pileup/cmdline_cmn.c                     |    6 +-
 tools/sra-pileup/dyn_string.c                      |   20 +
 tools/sra-pileup/dyn_string.h                      |    1 +
 tools/sra-pileup/inputfiles.c                      |    1 +
 tools/sra-pileup/md_flag.c                         |  268 ++
 .../{cg-dump/last_rowid.h => sra-pileup/md_flag.h} |   14 +-
 tools/sra-pileup/pileup_counters.c                 |    4 +-
 .../{pileup_varcount.c => pileup_indels.c}         |   71 +-
 .../vtblcp-priv.h => sra-pileup/pileup_indels.h}   |    8 +-
 tools/sra-pileup/pileup_options.h                  |    1 +
 tools/sra-pileup/pileup_v2.c                       |    8 +-
 tools/sra-pileup/pileup_varcount.c                 |   10 +-
 tools/sra-pileup/ref_regions.c                     |   74 +-
 tools/sra-pileup/ref_walker_0.c                    |   20 +-
 tools/sra-pileup/report_deletes.c                  |    2 +-
 tools/sra-pileup/reref.c                           |  208 +-
 tools/sra-pileup/sam-aligned.c                     |   44 +-
 tools/sra-pileup/sam-dump-opts.c                   |  171 +-
 tools/sra-pileup/sam-dump-opts.h                   |    3 +
 tools/sra-pileup/sam-dump.c                        |   14 +-
 tools/sra-pileup/sam-dump.vers                     |    2 +-
 tools/sra-pileup/sam-dump.vers.h                   |    2 +-
 tools/sra-pileup/sam-dump2.vers                    |    2 +-
 tools/sra-pileup/sam-dump3.c                       |   12 +-
 tools/sra-pileup/sam-hdr.c                         |    4 +-
 tools/sra-pileup/sam-hdr1.c                        |  853 ++++
 .../last_rowid.h => sra-pileup/sam-hdr1.h}         |   18 +-
 tools/sra-pileup/sra-pileup.c                      |  214 +-
 tools/sra-pileup/sra-pileup.vers                   |    2 +-
 tools/sra-pileup/sra-pileup.vers.h                 |    2 +-
 tools/sra-pileup/walk_debug.c                      |   75 +-
 tools/{sam-dump => sra-seq-count}/Makefile         |   53 +-
 tools/sra-seq-count/main_fkt.c                     |  211 +
 .../last_rowid.h => sra-seq-count/options.h}       |   24 +-
 tools/sra-seq-count/range.hpp                      |  307 ++
 tools/sra-seq-count/sra-seq-count.cpp              |  688 +++
 tools/sra-seq-count/sra-seq-count.vers             |    1 +
 tools/sra-sort/col-pair.c                          |    2 +-
 tools/sra-sort/idx-mapping.c                       |   12 +-
 tools/sra-sort/idx-mapping.h                       |    4 +-
 tools/sra-sort/meta-pair.c                         |   12 +-
 tools/sra-sort/poslen-col-pair.c                   |    2 +-
 tools/sra-sort/ref-alignid-col.c                   |   13 +-
 tools/sra-sort/sra-sort.c                          |   10 +-
 tools/sra-sort/sra-sort.vers                       |    2 +-
 tools/sra-stat/Makefile                            |    8 +-
 tools/sra-stat/sra-stat.c                          | 1301 ++++--
 .../{run-stat/mod_reads.h => sra-stat/sra-stat.h}  |   26 +-
 tools/sra-stat/sra-stat.vers                       |    2 +-
 tools/sra-stat/sra-stat.vers.h                     |    2 +-
 tools/sra-stat/sra.c                               |  446 ++
 tools/sra/.cvsignore                               |    1 +
 tools/sra/Makefile                                 |    9 +-
 tools/sra/table-vers.c                             |    4 +-
 tools/sra/table-vers.vers                          |    2 +-
 tools/srapath/srapath.c                            |   51 +-
 tools/srapath/srapath.vers                         |    2 +-
 tools/srapath/srapath.vers.h                       |    2 +-
 tools/update-schema/.cvsignore                     |    1 +
 tools/update-schema/Makefile                       |    4 +-
 tools/update-schema/update-schema.c                |   14 +-
 tools/update-schema/vdb-update-schema.vers         |    2 +-
 tools/util/Makefile                                |   39 +-
 tools/util/crc32sum.c                              |    2 +-
 tools/util/kdb-index.c                             |  264 ++
 tools/util/kdb-index.vers                          |    1 +
 tools/util/kdbmeta.c                               |   10 +-
 tools/util/kdbmeta.vers                            |    2 +-
 tools/util/kdbmeta.vers.h                          |    2 +-
 tools/util/md5cp.c                                 |    8 +-
 tools/util/md5cp.vers                              |    2 +-
 tools/util/md5cp.vers.h                            |    2 +-
 tools/util/pacbio-correct.c                        |    2 +-
 tools/util/pacbio-correct.vers                     |    2 +-
 tools/util/rcexplain.c                             |    2 +-
 tools/util/rcexplain.vers                          |    2 +-
 tools/util/rcexplain.vers.h                        |    2 +-
 tools/util/rowwritetest.c                          |    4 +-
 tools/util/rowwritetest.vers                       |    2 +-
 tools/{sra-sort/idx-mapping.h => util/samview.c}   |   74 +-
 tools/util/schema-replace.c                        |    4 +-
 tools/util/schema-replace.vers                     |    2 +-
 tools/util/schema-replace.vers.h                   |    2 +-
 tools/util/sortreadtest.c                          |    6 +-
 tools/util/test-sra.c                              | 1129 ++++-
 tools/util/test-sra.vers                           |    2 +-
 tools/util/test-sra.vers.h                         |    2 +-
 tools/util/testld.c                                |    4 +-
 tools/util/testld.vers                             |    2 +-
 tools/util/txt2kdb.c                               |    8 +-
 tools/util/txt2kdb.vers                            |    2 +-
 tools/util/vdb-lock.c                              |    2 +-
 tools/util/vdb-lock.vers                           |    2 +-
 tools/util/vdb-lock.vers.h                         |    2 +-
 tools/util/vdb-passwd.c                            |   46 +-
 tools/util/vdb-passwd.vers                         |    2 +-
 tools/util/vdb-passwd.vers.h                       |    2 +-
 tools/util/vdb-unlock.c                            |    2 +-
 tools/util/vdb-unlock.vers                         |    2 +-
 tools/util/vdb-unlock.vers.h                       |    2 +-
 tools/vcf-loader/.gitignore                        |    1 +
 tools/vcf-loader/Makefile                          |    9 +-
 tools/vcf-loader/vcf-database.c                    |    5 +-
 tools/vcf-loader/vcf-grammar.c                     |    2 +-
 tools/vcf-loader/vcf-grammar.y                     |    2 +-
 tools/vcf-loader/vcf-lex.c                         |   50 +-
 tools/vcf-loader/vcf-lex.l                         |   12 +-
 tools/vcf-loader/vcf-load.vers                     |    2 +-
 tools/vcf-loader/vcf-parse.h                       |    5 +-
 tools/vdb-config/configure.cpp                     |   56 +-
 tools/vdb-config/interactive.cpp                   |   64 +-
 tools/vdb-config/util.cpp                          |   93 +-
 tools/vdb-config/util.hpp                          |    7 +-
 tools/vdb-config/vdb-config-model.cpp              |   16 +-
 tools/vdb-config/vdb-config-model.hpp              |   75 +-
 tools/vdb-config/vdb-config.c                      |  921 ++--
 tools/vdb-config/vdb-config.vers                   |    2 +-
 tools/vdb-config/vdb-config.vers.h                 |    2 +-
 tools/vdb-copy/Makefile                            |    2 -
 tools/vdb-copy/context.c                           |   17 +-
 tools/vdb-copy/context.h                           |    5 +-
 tools/vdb-copy/definitions.h                       |    4 +
 tools/vdb-copy/num-gen.c                           |    4 +-
 tools/vdb-copy/progressbar.c                       |  137 -
 tools/vdb-copy/progressbar.h                       |   70 -
 tools/vdb-copy/type_matcher.c                      |   12 +-
 tools/vdb-copy/vdb-copy.c                          |   50 +-
 tools/vdb-copy/vdb-copy.vers                       |    2 +-
 tools/vdb-copy/vdb-copy.vers.h                     |    2 +-
 tools/vdb-decrypt/shared.c                         |   17 +-
 tools/vdb-decrypt/vdb-decrypt.vers                 |    2 +-
 tools/vdb-decrypt/vdb-decrypt.vers.h               |    2 +-
 tools/vdb-decrypt/vdb-encrypt.vers                 |    2 +-
 tools/vdb-decrypt/vdb-encrypt.vers.h               |    2 +-
 tools/{sra-dbcc => vdb-diff}/Makefile              |   33 +-
 tools/vdb-diff/coldefs.c                           |  211 +
 .../vdb-dump-num-gen.h => vdb-diff/coldefs.h}      |   87 +-
 tools/vdb-diff/namelist_tools.c                    |  299 ++
 .../sg_lookup.h => vdb-diff/namelist_tools.h}      |   40 +-
 tools/vdb-diff/vdb-diff.c                          | 1017 ++++
 tools/vdb-diff/vdb-diff.vers                       |    1 +
 tools/vdb-diff/vdb-diff.vers.h                     |    1 +
 tools/vdb-dump/Makefile                            |    1 -
 tools/vdb-dump/help.txt                            |  194 +-
 tools/vdb-dump/vdb-boot.vers                       |    2 +-
 tools/vdb-dump/vdb-dump-bin.c                      |  397 +-
 tools/vdb-dump/vdb-dump-bin.h                      |    2 +
 tools/vdb-dump/vdb-dump-coldefs.c                  |  180 +-
 tools/vdb-dump/vdb-dump-coldefs.h                  |    5 +
 tools/vdb-dump/vdb-dump-context.c                  |   60 +-
 tools/vdb-dump/vdb-dump-context.h                  |   26 +-
 tools/vdb-dump/vdb-dump-fastq.c                    |  958 ++--
 tools/vdb-dump/vdb-dump-formats.c                  |   58 +-
 tools/vdb-dump/vdb-dump-helper.c                   |  118 +-
 tools/vdb-dump/vdb-dump-helper.h                   |    5 +-
 tools/vdb-dump/vdb-dump-num-gen.c                  |  477 --
 tools/vdb-dump/vdb-dump-row-context.h              |    2 +-
 tools/vdb-dump/vdb-dump-str.c                      |  160 +
 tools/vdb-dump/vdb-dump-str.h                      |    5 +
 tools/vdb-dump/vdb-dump-tools.c                    |    7 +-
 tools/vdb-dump/vdb-dump-tools.h                    |    2 +-
 tools/vdb-dump/vdb-dump.c                          |  778 +++-
 tools/vdb-dump/vdb-dump.vers                       |    2 +-
 tools/vdb-dump/vdb-dump.vers.h                     |    2 +-
 tools/vdb-dump/vdb_info.c                          |  462 +-
 tools/vdb-dump/vdb_info.h                          |    2 +-
 tools/vdb-validate/vdb-validate.c                  |   92 +-
 tools/vdb-validate/vdb-validate.vers               |    2 +-
 tools/vdb-validate/vdb-validate.vers.h             |    2 +-
 tools/vdbview/b_first.png                          |  Bin 528 -> 0 bytes
 tools/vdbview/b_goto.png                           |  Bin 475 -> 0 bytes
 tools/vdbview/b_last.png                           |  Bin 519 -> 0 bytes
 tools/vdbview/b_next.png                           |  Bin 428 -> 0 bytes
 tools/vdbview/b_nextpage.png                       |  Bin 639 -> 0 bytes
 tools/vdbview/b_prev.png                           |  Bin 426 -> 0 bytes
 tools/vdbview/b_prevpage.png                       |  Bin 636 -> 0 bytes
 tools/vdbview/b_search.png                         |  Bin 614 -> 0 bytes
 tools/vdbview/background.pas                       |  277 --
 tools/vdbview/buttons.svg                          |  268 --
 tools/vdbview/columnsel.lfm                        |   90 -
 tools/vdbview/columnsel.pas                        |  115 -
 tools/vdbview/dataproxy.pas                        |  602 ---
 tools/vdbview/gotoform.lfm                         |   56 -
 tools/vdbview/gotoform.pas                         |   47 -
 tools/vdbview/jobdef.pas                           |   27 -
 tools/vdbview/linkedlist.pas                       |  186 -
 tools/vdbview/logo_128.png                         |  Bin 1752 -> 0 bytes
 tools/vdbview/logo_16.png                          |  Bin 368 -> 0 bytes
 tools/vdbview/logo_256.png                         |  Bin 3524 -> 0 bytes
 tools/vdbview/logo_32.png                          |  Bin 541 -> 0 bytes
 tools/vdbview/logo_64.png                          |  Bin 910 -> 0 bytes
 tools/vdbview/mainwindow.lfm                       |  973 ----
 tools/vdbview/mainwindow.pas                       |  793 ----
 tools/vdbview/searchform.lfm                       |   69 -
 tools/vdbview/searchform.pas                       |   79 -
 tools/vdbview/selector_types.pas                   |   20 -
 tools/vdbview/support_unit.pas                     |  217 -
 tools/vdbview/svdb.pas                             |  676 ---
 tools/vdbview/svdb_obj.pas                         |  339 --
 tools/vdbview/vdbview.ico                          |  Bin 25890 -> 0 bytes
 tools/vdbview/vdbview.lpi                          |  343 --
 tools/vdbview/vdbview.lpr                          |   24 -
 tools/vdbview/vdbview.res                          |  Bin 27156 -> 0 bytes
 tools/vdbview/vdbview1.ico                         |  Bin 25890 -> 0 bytes
 tools/vdbview/version.lfm                          |   40 -
 tools/vdbview/version.pas                          |   33 -
 tools/vtblcp/vtblcp.c                              |  979 ----
 tools/vtblcp/vtblcp.vers                           |    1 -
 tools/workspace/.gitignore                         |    3 -
 tools/workspace/path-to-kar-file.cpp               |  117 -
 tools/workspace/prefs-lex.l                        |  181 -
 tools/workspace/prefs-yacc.y                       |  189 -
 tools/workspace/sra.cpp                            | 1514 ------
 tools/workspace/sra.vers                           |    1 -
 tools/workspace/sratoolkit-exception.cpp           |  126 -
 tools/workspace/sratoolkit-exception.hpp           |  111 -
 tools/workspace/token.c                            |  228 -
 tools/workspace/token.h                            |   99 -
 tools/workspace/workspace.cpp                      | 1116 -----
 win-configure.bat                                  |    1 -
 753 files changed, 58090 insertions(+), 42735 deletions(-)

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