[med-svn] [sra-sdk] branch master updated (ccb209d -> bad95ef)

Andreas Tille tille at debian.org
Tue Aug 13 12:52:07 UTC 2013


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

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

      from  ccb209d   Merge tag 'upstream/2.3.2-4'
       new  bad95ef   Revert "Merge tag 'upstream/2.3.2-4'"

The 1 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:
 tools/sra-sort/Makefile.clang => CHANGES           |    5 +-
 Makefile                                           |   45 +-
 README                                             |   22 +-
 README-WINDOWS.txt                                 |   15 -
 README-build.txt => README-build                   |  148 +-
 README-config.txt                                  |   58 -
 USAGE                                              |  162 +
 build/BUILD.linux                                  |    2 +-
 build/BUILD.mac                                    |    2 +-
 build/BUILD.win                                    |    2 +-
 build/COMP.mac                                     |    2 +-
 build/LNKG.linux                                   |    1 -
 build/LNKG.mac                                     |    1 -
 build/LNKG.win                                     |    1 -
 build/Makefile.clang                               |   80 -
 build/Makefile.env                                 |  140 +-
 build/Makefile.gcc                                 |   18 +-
 build/Makefile.linux                               |    7 -
 build/Makefile.mac                                 |    7 -
 build/Makefile.rules                               |    5 +
 build/Makefile.shell                               |  102 +-
 build/Makefile.vc++                                |   22 +-
 build/Makefile.win                                 |    7 -
 libs/krypto/rng-priv.h => build/STATIC             |    0
 build/ld.linux.cmn.sh                              |    6 +-
 build/ld.linux.dlib.sh                             |    4 -
 build/ld.linux.exe.sh                              |    7 +-
 build/ld.linux.ln.sh                               |   13 +-
 build/ld.linux.slib.sh                             |    4 +-
 build/ld.mac.cmn.sh                                |   12 +-
 build/ld.mac.dlib.sh                               |  116 +-
 build/ld.mac.exe.sh                                |  118 +-
 build/ld.mac.ln.sh                                 |    2 -
 build/ld.mac.slib.sh                               |    6 +-
 build/ld.sh                                        |  272 +-
 build/ld.win.cmn.sh                                |    7 +-
 build/ld.win.dlib.sh                               |   60 +-
 build/ld.win.exe.sh                                |    6 +-
 build/ld.win.slib.sh                               |   51 +-
 build/mac.arch.sh                                  |    9 +-
 build/sra-dflt-schema.sh                           |   50 +-
 build/win-cc.sh                                    |  110 +-
 configuration-assistant.perl                       | 1266 +-
 .../{bam-load-help.html => bam-loader-help.html}   |    6 +-
 doc/help/html/crc32sum-help.html                   |    2 +-
 interfaces/align/align-access.h                    |   11 +-
 interfaces/align/align.vschema                     |  675 +-
 interfaces/{kproc/timeout.h => align/alignarc.h}   |   29 +-
 interfaces/align/bam.h                             |   91 +-
 interfaces/align/dna-reverse-cmpl.h                |   43 -
 interfaces/align/iterator.h                        |  610 -
 interfaces/align/manager.h                         |   69 -
 interfaces/align/qstat.vschema                     |   87 -
 interfaces/align/quality-quantizer.h               |   49 -
 interfaces/align/reader-refseq.h                   |    6 +-
 interfaces/align/reference.h                       |  150 -
 interfaces/align/refseq-mgr.h                      |   16 +-
 interfaces/align/refseq.vschema                    |  100 -
 interfaces/align/seq.vschema                       |  300 -
 interfaces/align/writer-alignment.h                |   49 +-
 interfaces/align/writer-reference.h                |   45 +-
 interfaces/align/writer-refseq.h                   |    6 +-
 interfaces/align/writer-sequence.h                 |   16 +-
 interfaces/cc/gcc/i386/atomic.h                    |    1 -
 interfaces/cc/gcc/i386/{bitstr.h => fmtdef.h}      |   23 +-
 interfaces/cc/gcc/noarch/bitstr.h                  |   29 +-
 interfaces/cc/gcc/v128.h                           | 1088 -
 .../cc/gcc/x86_64/fmtdef.h                         |   49 +-
 interfaces/cc/vc++/compiler.h                      |    2 +-
 interfaces/cc/vc++/i386/arch-impl.h                |  194 +
 .../cc/{gcc/i386/bitstr.h => vc++/i386/fmtdef.h}   |   23 +-
 interfaces/cc/vc++/noarch/arch-impl.h              |  194 -
 interfaces/cc/vc++/noarch/bitstr.h                 |    8 +-
 interfaces/cc/vc++/stdint.h                        |   43 +-
 interfaces/cc/vc++/x86_64/arch-impl.h              |  133 +
 .../cc/{gcc/i386/bitstr.h => vc++/x86_64/fmtdef.h} |   22 +-
 interfaces/ext/libxml/DOCBparser.h                 |   96 -
 interfaces/ext/libxml/HTMLparser.h                 |  303 -
 interfaces/ext/libxml/HTMLtree.h                   |  147 -
 interfaces/ext/libxml/SAX.h                        |  173 -
 interfaces/ext/libxml/SAX2.h                       |  176 -
 interfaces/ext/libxml/c14n.h                       |  115 -
 interfaces/ext/libxml/catalog.h                    |  182 -
 interfaces/ext/libxml/chvalid.h                    |  230 -
 interfaces/ext/libxml/debugXML.h                   |  217 -
 interfaces/ext/libxml/dict.h                       |   69 -
 interfaces/ext/libxml/encoding.h                   |  226 -
 interfaces/ext/libxml/entities.h                   |  150 -
 interfaces/ext/libxml/globals.h                    |  491 -
 interfaces/ext/libxml/hash.h                       |  233 -
 interfaces/ext/libxml/list.h                       |  137 -
 interfaces/ext/libxml/nanoftp.h                    |  143 -
 interfaces/ext/libxml/nanohttp.h                   |   81 -
 interfaces/ext/libxml/parser.h                     | 1226 -
 interfaces/ext/libxml/parserInternals.h            |  611 -
 interfaces/ext/libxml/pattern.h                    |  100 -
 interfaces/ext/libxml/relaxng.h                    |  213 -
 interfaces/ext/libxml/schemasInternals.h           |  958 -
 interfaces/ext/libxml/schematron.h                 |  142 -
 interfaces/ext/libxml/threads.h                    |   84 -
 interfaces/ext/libxml/tree.h                       | 1252 -
 interfaces/ext/libxml/uri.h                        |   94 -
 interfaces/ext/libxml/valid.h                      |  458 -
 interfaces/ext/libxml/xinclude.h                   |  125 -
 interfaces/ext/libxml/xlink.h                      |  189 -
 interfaces/ext/libxml/xmlIO.h                      |  360 -
 interfaces/ext/libxml/xmlautomata.h                |  146 -
 interfaces/ext/libxml/xmlerror.h                   |  944 -
 interfaces/ext/libxml/xmlexports.h                 |  157 -
 interfaces/ext/libxml/xmlmemory.h                  |  224 -
 interfaces/ext/libxml/xmlmodule.h                  |   57 -
 interfaces/ext/libxml/xmlreader.h                  |  424 -
 interfaces/ext/libxml/xmlregexp.h                  |  222 -
 interfaces/ext/libxml/xmlsave.h                    |   87 -
 interfaces/ext/libxml/xmlschemas.h                 |  218 -
 interfaces/ext/libxml/xmlschemastypes.h            |  151 -
 interfaces/ext/libxml/xmlstring.h                  |  140 -
 interfaces/ext/libxml/xmlunicode.h                 |  202 -
 interfaces/ext/libxml/xmlversion.h                 |  458 -
 interfaces/ext/libxml/xmlwriter.h                  |  485 -
 interfaces/ext/libxml/xpath.h                      |  546 -
 interfaces/ext/libxml/xpathInternals.h             |  630 -
 interfaces/ext/libxml/xpointer.h                   |  114 -
 interfaces/insdc/insdc.h                           |   35 -
 interfaces/insdc/sra.h                             |   27 +-
 interfaces/insdc/sra.vschema                       |    1 -
 interfaces/kapp/args.h                             |   54 +-
 interfaces/kapp/loader-file.h                      |   17 +-
 interfaces/kapp/loader-meta.h                      |    2 +-
 interfaces/kapp/log-xml.h                          |   10 +-
 interfaces/kapp/queue-file.h                       |  149 -
 interfaces/kdb/btree.h                             |   95 +-
 interfaces/kdb/consistency-check.h                 |   21 +-
 interfaces/kdb/database.h                          |   18 +-
 interfaces/kdb/kdb-priv.h                          |   12 -
 interfaces/kdb/manager.h                           |   40 +-
 interfaces/kdb/namelist.h                          |    3 +-
 interfaces/kdb/table.h                             |   14 -
 interfaces/kfg/config.h                            |  168 +-
 interfaces/kfg/kfg-priv.h                          |    4 -
 interfaces/kfg/repository.h                        |  271 -
 interfaces/kfs/arc.h                               |   14 -
 interfaces/kfs/buffile.h                           |   10 -
 interfaces/kfs/cacheteefile.h                      |  147 -
 interfaces/kfs/directory.h                         |   63 +-
 interfaces/kfs/file.h                              |   29 -
 interfaces/kfs/impl.h                              |   11 +-
 interfaces/kfs/kfs-priv.h                          |   31 +-
 interfaces/kfs/lockfile.h                          |  116 -
 interfaces/{vfs => kfs}/path-priv.h                |   98 +-
 interfaces/{vfs => kfs}/path.h                     |   94 +-
 interfaces/kfs/quickmount.h                        |   61 -
 interfaces/kfs/ramfile.h                           |   75 -
 interfaces/kfs/readheadfile.h                      |   86 -
 interfaces/kfs/sra.h                               |   19 +-
 interfaces/kfs/tar.h                               |    5 -
 interfaces/klib/checksum.h                         |    2 +-
 interfaces/klib/debug.h                            |   33 +-
 interfaces/klib/defs.h                             |    7 +-
 interfaces/klib/extern.h                           |    6 +-
 interfaces/klib/klib-priv.h                        |  106 -
 interfaces/klib/ksort-macro.h                      |  257 -
 interfaces/klib/log.h                              |    4 +-
 interfaces/klib/namelist.h                         |   10 -
 interfaces/klib/out.h                              |    6 +-
 interfaces/klib/printf.h                           |  260 +-
 interfaces/klib/rc.h                               |  129 +-
 interfaces/klib/refcount.h                         |    8 +-
 interfaces/klib/report.h                           |   98 -
 interfaces/klib/sort.h                             |   60 -
 interfaces/klib/status.h                           |    2 +-
 interfaces/klib/vector.h                           |  155 -
 interfaces/{kxml => klib}/xml.h                    |   41 +-
 interfaces/klib/xml.hpp                            |  198 +
 interfaces/kns/KCurlRequest.h                      |   65 -
 interfaces/kns/curl-file.h                         |   49 -
 interfaces/kns/entrez-fetcher.h                    |   88 -
 interfaces/kns/extern.h                            |   41 -
 interfaces/kns/impl.h                              |  104 -
 interfaces/kns/manager.h                           |   85 -
 interfaces/kns/stream.h                            |  126 -
 interfaces/kns/url-fetcher.h                       |   66 -
 interfaces/kproc/impl.h                            |  104 -
 interfaces/kproc/procmgr.h                         |  115 -
 interfaces/kproc/q-extern.h                        |    4 +-
 interfaces/kproc/queue.h                           |    2 +-
 interfaces/kproc/sem.h                             |    8 -
 interfaces/kproc/task.h                            |   83 -
 interfaces/krypto/cipher-impl.h                    |    1 -
 interfaces/krypto/cipher-priv.h                    |    1 -
 interfaces/krypto/cipher-test.h                    |   49 -
 interfaces/krypto/cipher.h                         |  208 -
 interfaces/krypto/ciphermgr-priv.h                 |   38 -
 interfaces/krypto/ciphermgr.h                      |   98 -
 interfaces/krypto/encfile-priv.h                   |  250 -
 interfaces/krypto/encfile.h                        |  134 -
 interfaces/krypto/extern.h                         |   66 -
 interfaces/krypto/key.h                            |  103 -
 interfaces/krypto/manager-priv.h                   |   26 -
 interfaces/krypto/manager.h                        |   33 -
 interfaces/krypto/reencfile.h                      |   91 -
 interfaces/krypto/rng-impl.h                       |   86 -
 interfaces/krypto/rng.h                            |   68 -
 interfaces/krypto/testciphermgr.h                  |   58 -
 interfaces/krypto/wgaencrypt.h                     |  128 -
 interfaces/ktst/test_tools.hpp                     |   93 +-
 interfaces/ktst/unit_test.hpp                      |  283 +-
 interfaces/ktst/unit_test_suite.hpp                |  524 +-
 interfaces/loader/alignment-writer.h               |   97 -
 interfaces/loader/common-reader-priv.h             |  300 -
 interfaces/loader/common-reader.h                  |  486 -
 interfaces/loader/common-writer.h                  |  190 -
 interfaces/loader/mmarray.h                        |   50 -
 interfaces/loader/reference-writer.h               |   78 -
 interfaces/loader/sequence-writer.h                |   91 -
 interfaces/ncbi/seq.vschema                        |   27 +-
 interfaces/ncbi/wgs-contig.h                       |  176 -
 interfaces/ncbi/wgs-contig.vschema                 |  660 -
 interfaces/os/mac/os-native.h                      |    6 +-
 interfaces/os/unix/unix-native.h                   |   13 +
 interfaces/os/win/atomic64.h                       |   34 +-
 interfaces/os/win/os-native.h                      |   59 +-
 interfaces/sra/impl.h                              |   20 -
 interfaces/sra/pevents.vschema                     |    2 +-
 interfaces/sra/sradb-priv.h                        |  123 +-
 interfaces/sra/srapath.h                           |    9 +-
 interfaces/vdb/blob.h                              |  147 -
 interfaces/vdb/built-in.vschema                    |   26 +-
 interfaces/vdb/cursor.h                            |   37 -
 interfaces/vdb/database.h                          |   18 +-
 interfaces/vdb/dependencies.h                      |  211 -
 interfaces/vdb/manager.h                           |   23 -
 interfaces/vdb/manager.hpp                         |    8 +-
 interfaces/vdb/report.h                            |   92 -
 interfaces/vdb/vdb-priv.h                          |   70 +-
 interfaces/vdb/vdb.vschema                         |   59 +-
 interfaces/vfs/extern.h                            |   42 -
 interfaces/vfs/manager-priv.h                      |  115 -
 interfaces/vfs/manager.h                           |  306 -
 interfaces/vfs/resolver.h                          |  206 -
 libs/Makefile                                      |   19 +-
 libs/align/Makefile                                |   39 +-
 libs/align/al_iterator.c                           |  562 -
 libs/align/align-access.c                          |   22 +-
 libs/align/align_mgr.c                             |  108 -
 libs/align/bam.c                                   | 2933 +-
 libs/align/debug.h                                 |   36 +-
 libs/align/dna-reverse-cmpl.c                      |   80 -
 libs/align/libalign-access.vers                    |    2 +-
 libs/align/libalign-reader.vers                    |    2 +-
 .../libkns.vers => align/libalign-writer.vers}     |    0
 libs/align/pl_iterator.c                           |  671 -
 libs/align/quality-quantizer.c                     |  105 -
 libs/align/reader-cmn.c                            |  290 +-
 libs/align/reader-cmn.h                            |   31 +-
 libs/align/reader-refseq.c                         |  103 +-
 libs/align/ref_iterator.c                          |  866 -
 libs/align/reference-cmn.c                         |   43 -
 libs/align/reference-cmn.h                         |   38 -
 libs/align/reference.c                             | 1933 -
 libs/align/refseq-mgr.c                            |  626 +-
 libs/align/writer-alignment.c                      |  128 +-
 libs/align/writer-cmn.c                            |  112 +-
 libs/align/writer-priv.h                           |   10 +-
 libs/align/writer-ref.c                            |  175 +-
 libs/align/writer-ref.h                            |   22 +-
 libs/align/writer-reference.c                      | 2987 +-
 libs/align/writer-refseq.c                         |   19 +-
 libs/align/writer-sequence.c                       |  221 +-
 libs/axf/Makefile                                  |   25 +-
 libs/axf/align-local_ref_id.c                      |   70 +-
 libs/axf/align-local_ref_start.c                   |   61 +-
 libs/axf/align-ref-name.c                          |   52 +-
 libs/axf/align-ref-pos.c                           |  147 +-
 libs/axf/align-ref-seq-id.c                        |   60 +-
 libs/axf/align-restore-read.c                      |   28 +-
 libs/axf/cigar.c                                   | 1089 +-
 libs/axf/get-sam-flags.c                           |   80 +-
 libs/axf/get_mate_align_ids.c                      |  271 -
 libs/axf/libaxf.vers                               |    2 +-
 libs/axf/libaxf.vers.h                             |    1 +
 libs/axf/libwaxf.vers                              |    2 +-
 libs/axf/libwaxf.vers.h                            |    1 +
 libs/axf/make-cmp-read_desc.c                      |  156 -
 libs/axf/not-my-row.c                              |    2 +-
 libs/axf/project_read_from_sequence.c              |  119 +-
 libs/axf/ref-preserve_qual.c                       |    2 -
 libs/axf/ref-restore-read.c                        |    6 +-
 libs/axf/ref-tbl-sub-select.c                      |  471 +-
 libs/axf/ref-tbl.c                                 |   85 -
 libs/axf/ref-tbl.h                                 |   32 -
 libs/axf/refseq-stats.c                            |    2 +-
 libs/axf/seq-construct-read.c                      |  125 -
 libs/axf/seq-restore-read.c                        |   92 +-
 libs/axf/template-len.c                            |  112 +-
 libs/ext/Makefile                                  |    3 +-
 libs/ext/bzip2/Makefile                            |   93 +-
 libs/ext/bzip2/blocksort.c                         | 1094 -
 libs/ext/bzip2/bzip2-1.0.6.tar.gz                  |  Bin 782025 -> 0 bytes
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 libs/ext/zlib/Makefile                             |   97 +-
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 libs/kdb/wmeta.c                                   |   90 +-
 libs/kdb/wtable.c                                  |  186 +-
 libs/kdb/wtrieidx-v1.c                             |    2 +-
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 .../Makefile.gcc => libs/kfg/config.linux.kfg      |    6 +-
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