[Debian-med-packaging] sra-sdk git repository totally screwed up - I start from scratch and leave sra-sdk_.git for some time if somebody really cares about the history [Was: branch upstream updated (ba954f7 -> 46a4f38)]
Andreas Tille
andreas at an3as.eu
Tue Aug 13 13:51:03 UTC 2013
Hi,
I screwed up the Git repository of sra-sdk totally. Even after import
of a new upstream the old code remains in master. I tried to get some
help of Git experts here around but we all failed. Because I fail to
see the use for our users if I spend hours for fixing it I decide to
start from scratch and leave some backup at git.debian.org. If somebody
really wants to spend some time into it I'd volunteer to inject all my
changes into a fixed reporitory.
Sorry for the inconvience I'd try my best to avoid things like this in
the future.
Kind regards
Andreas.
----- Forwarded message from Andreas Tille <tille at debian.org> -----
Date: Tue, 13 Aug 2013 13:34:26 +0000
From: Andreas Tille <tille at debian.org>
To: debian-med-commit at lists.alioth.debian.org
Subject: [sra-sdk] branch upstream updated (ba954f7 -> 46a4f38)
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository sra-sdk.
from ba954f7 Revert "Imported Upstream version 2.3.2-4"
new 228e4f2 Imported Upstream version 2.3.2-4+dfsg
new becf6a3 Imported Upstream version 2.3.2-4+dfsg
new 46a4f38 Imported Upstream version 2.3.2-4+dfsg
The 3 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:
CHANGES | 30 -
Makefile | 45 +-
README | 22 +-
README-WINDOWS.txt | 15 +
README-build | 237 -
README-build.txt | 259 +
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 +
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 +-
doc/help/html/bam-load-help.html | 29 +
doc/help/html/bam-loader-help.html | 31 -
doc/help/html/crc32sum-help.html | 2 +-
interfaces/align/align-access.h | 11 +-
interfaces/align/align.vschema | 675 +-
interfaces/align/alignarc.h | 63 -
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/fmtdef.h | 42 -
interfaces/cc/gcc/noarch/bitstr.h | 29 +-
interfaces/cc/gcc/v128.h | 1088 +
interfaces/cc/gcc/x86_64/fmtdef.h | 58 -
interfaces/cc/vc++/compiler.h | 2 +-
interfaces/cc/vc++/i386/arch-impl.h | 194 -
interfaces/cc/vc++/i386/fmtdef.h | 42 -
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 -
interfaces/cc/vc++/x86_64/fmtdef.h | 41 -
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/kfs/path-priv.h | 101 -
interfaces/kfs/path.h | 237 -
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/klib/xml.h | 355 -
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/kproc/timeout.h | 64 +
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/kxml/xml.h | 382 +
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/path-priv.h | 149 +
interfaces/vfs/path.h | 289 +
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 | 2883 +-
libs/align/debug.h | 36 +-
libs/align/dna-reverse-cmpl.c | 80 +
libs/align/libalign-access.vers | 2 +-
libs/align/libalign-reader.vers | 2 +-
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 | 101 -
libs/ext/bzip2/Makefile | 166 -
libs/ext/zlib/Makefile | 175 -
libs/kapp/Makefile | 10 +
libs/kapp/args.c | 749 +-
libs/kapp/args_debug.h | 47 +
libs/kapp/libload.vers | 2 +-
libs/kapp/loader-file.c | 117 +-
libs/kapp/log-xml.c | 26 +-
libs/kapp/main.c | 36 +-
libs/kapp/queue-file.c | 925 +
libs/kapp/tokenizer.c | 525 +
libs/kapp/unix/sysmain.c | 13 +
libs/kapp/win/sysmain.c | 18 +
libs/kdb/Makefile | 20 +-
libs/kdb/btree.c | 69 +-
libs/kdb/coldata.c | 2 +-
libs/kdb/colidx0.c | 4 +-
libs/kdb/colidx1.c | 8 +-
libs/kdb/colidx2-priv.h | 29 +-
libs/kdb/colidx2.c | 114 +-
libs/kdb/column-cc.c | 67 +-
libs/kdb/column.c | 26 +-
libs/kdb/database-cc.c | 232 +-
libs/kdb/database-cmn.c | 2 +-
libs/kdb/database.c | 198 +-
libs/kdb/dbcc-cmn.c | 2 +-
libs/kdb/dbmgr-cmn.c | 62 +-
libs/kdb/dbmgr-priv.h | 5 +-
libs/kdb/dbmgr.c | 255 +-
libs/kdb/idxblk.c | 9 +-
libs/kdb/index-cmn.h | 7 +-
libs/kdb/index.c | 16 +-
libs/kdb/kdb-priv.h | 45 +-
libs/kdb/kdb.c | 652 +-
libs/kdb/libkdb.vers | 2 +-
libs/kdb/libkdb.vers.h | 1 -
libs/kdb/libwkdb.vers | 2 +-
libs/kdb/libwkdb.vers.h | 1 -
libs/kdb/meta.c | 69 +-
libs/kdb/ptrieval-v2.c | 115 +-
libs/kdb/table-cc.c | 229 +-
libs/kdb/table.c | 133 +-
libs/kdb/trieidx-v2.c | 21 +-
libs/kdb/trieval-v2.c | 4 +-
libs/kdb/wcolidx0.c | 4 +-
libs/kdb/wcolidx1.c | 10 +-
libs/kdb/wcolidx2.c | 6 +-
libs/kdb/wcolumn.c | 74 +-
libs/kdb/wdatabase.c | 233 +-
libs/kdb/wdbmgr.c | 15 +-
libs/kdb/windex.c | 16 +-
libs/kdb/wkdb-priv.h | 62 +-
libs/kdb/wkdb.c | 653 +-
libs/kdb/wmeta.c | 90 +-
libs/kdb/wtable.c | 186 +-
libs/kdb/wtrieidx-v1.c | 2 +-
libs/kdb/wtrieidx-v2.c | 14 +-
libs/kfg/Makefile | 43 +-
libs/kfg/config-grammar.c | 1725 +
libs/kfg/config-lex.c | 2511 +
libs/kfg/config-tokens.h | 75 +
libs/kfg/config.c | 2309 +-
libs/kfg/config.linux.kfg | 29 -
libs/kfg/config.mac.kfg | 29 -
libs/kfg/config.win.kfg | 29 -
libs/kfg/default.kfg | 45 +
libs/kfg/kfg-parse.h | 81 +
libs/kfg/libkfg.vers | 2 +-
libs/kfg/report-kfg.c | 505 +
libs/kfg/report.c | 433 +
libs/kfg/repository.c | 1087 +
libs/kfs/Makefile | 24 +-
libs/kfs/arc.c | 273 +-
libs/kfs/buffile-read.c | 265 +
libs/kfs/buffile-write.c | 4 +-
libs/kfs/buffile.c | 2 +-
libs/kfs/bzip.c | 34 +-
libs/kfs/cacheteefile.c | 1689 +
libs/kfs/countfile.c | 11 +
libs/kfs/crc32.c | 19 +-
libs/kfs/directory.c | 183 +-
libs/kfs/ffext.c | 12 +-
libs/kfs/ffmagic.c | 122 +-
libs/kfs/file.c | 160 +-
libs/kfs/fileformat-priv.h | 2 +-
libs/kfs/gzip.c | 5 +-
libs/kfs/libkfs.vers | 2 +-
libs/kfs/lockfile.c | 350 +
libs/kfs/md5.c | 42 +-
libs/kfs/mmap.c | 12 +-
libs/kfs/nullfile.c | 1 +
libs/kfs/pagefile.c | 121 +-
libs/kfs/path-priv.h | 114 -
libs/kfs/path.c | 1669 -
libs/kfs/quickmount.c | 967 +
libs/kfs/ramfile.c | 415 +
libs/kfs/readheadfile.c | 294 +
libs/kfs/report.c | 169 +
libs/kfs/sra.c | 79 +-
libs/kfs/subfile.c | 18 +-
libs/kfs/tar.c | 94 +-
libs/kfs/teefile.c | 1 +
libs/kfs/tocentry.c | 39 +-
libs/kfs/tocfile.c | 2 +-
libs/kfs/unix/sysdir-priv.h | 9 -
libs/kfs/unix/sysdir.c | 94 +-
libs/kfs/unix/sysdll.c | 120 +-
libs/kfs/unix/sysfile-priv.h | 2 +-
libs/kfs/unix/sysfile.c | 24 +-
libs/kfs/unix/syslockfile.c | 215 +
libs/kfs/unix/syspath.c | 126 -
libs/kfs/win/lnk_tools.c | 9 +-
libs/kfs/win/sysdir-priv.h | 4 +-
libs/kfs/win/sysdir.c | 254 +-
libs/kfs/win/sysdll.c | 115 +-
libs/kfs/win/sysfile-priv.h | 5 +-
libs/kfs/win/sysfile.c | 347 +-
libs/kfs/win/syslockfile.c | 67 +
libs/kfs/win/sysmmap.c | 2 +
libs/kfs/win/syspath.c | 287 -
libs/klib/Judy.h | 629 +
libs/klib/Makefile | 36 +-
libs/klib/SHA-32bit.c | 8 +-
libs/klib/SHA-64bit.c | 8 +-
libs/klib/data-buffer.c | 223 +-
libs/klib/judy-vector.c | 892 +
libs/klib/judy/Judy1.h | 549 +
libs/klib/judy/JudyByCount.c | 952 +
libs/klib/judy/JudyByCountWithDefs.c | 4 +
libs/klib/judy/JudyCascade.c | 1940 +
libs/klib/judy/JudyCount.c | 1193 +
libs/klib/judy/JudyCreateBranch.c | 312 +
libs/klib/judy/JudyDecascade.c | 1204 +
libs/klib/judy/JudyDel.c | 2144 +
libs/klib/judy/JudyFirst.c | 211 +
libs/klib/judy/JudyFreeArray.c | 361 +
libs/klib/judy/JudyGet.c | 1092 +
libs/klib/judy/JudyHS.c | 770 +
libs/klib/judy/JudyHS.h | 35 +
libs/klib/judy/JudyIns.c | 1871 +
libs/klib/judy/JudyInsArray.c | 1176 +
libs/klib/judy/JudyInsertBranch.c | 133 +
libs/klib/judy/JudyL.h | 503 +
libs/klib/judy/JudyMalloc.c | 86 +
libs/klib/judy/JudyMallocIF.c | 780 +
libs/klib/judy/JudyMemActive.c | 257 +
libs/klib/judy/JudyMemUsed.c | 59 +
libs/klib/judy/JudyNext.c | 2 +
libs/klib/judy/JudyNextEmpty.c | 2 +
libs/klib/judy/JudyPrev.c | 2 +
libs/klib/judy/JudyPrevEmpty.c | 2 +
libs/klib/judy/JudyPrevNext.c | 1888 +
libs/klib/judy/JudyPrevNextEmpty.c | 1388 +
libs/klib/judy/JudyPrintJP.c | 399 +
libs/klib/judy/JudyPrivate.h | 1610 +
libs/klib/judy/JudyPrivate1L.h | 483 +
libs/klib/judy/JudyPrivateBranch.h | 777 +
libs/klib/judy/JudySL.c | 1125 +
libs/klib/judy/JudyTablesGen.c | 294 +
libs/klib/judy/Makefile | 207 +
libs/klib/judy/j__udyGet.c | 2 +
libs/klib/ksort.c | 97 +
libs/klib/libklib.vers | 2 +-
libs/klib/libklib.vers.h | 1 -
libs/klib/log.c | 40 +-
libs/klib/pbstree-impl.c | 220 +-
libs/klib/printf.c | 2329 +-
libs/klib/qsort.c | 34 +-
libs/klib/refcount.c | 1 -
libs/klib/report.c | 816 +
libs/klib/status.c | 4 +-
libs/klib/symtab.c | 2 +-
libs/klib/token.c | 9 +-
libs/klib/unix/systime.c | 4 +-
libs/klib/unpack.c | 176 +-
libs/klib/vector_namelist.c | 57 +
libs/klib/vlen-encode.c | 3 +-
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libs/kns/curlhdr/curl.h | 1600 +
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libs/krypto/aes-ncbi-priv.h | 227 +
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libs/krypto/aes-ncbi.c | 2644 +
libs/krypto/aes-ncbi.vec.pic.o.list |74023 +++++++++++++++++++
libs/krypto/aes-ncbi.vecreg.pic.o.list |75192 ++++++++++++++++++++
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libs/krypto/aes_core.c | 1181 +
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libs/krypto/cipher-priv.h | 79 +
libs/krypto/cipher-vec.aes-ni.pic.o.list |10909 +++
libs/krypto/cipher-vec.c | 808 +
libs/krypto/cipher-vec.vec.pic.o.list |10959 +++
libs/krypto/cipher-vec.vecreg.pic.o.list |10919 +++
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libs/krypto/ciphermgr.c | 295 +
libs/krypto/compile-test.aes-ni.pic.o.list | 592 +
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libs/krypto/encfilev2.c | 2589 +
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libs/krypto/null-ncbi-priv.h | 56 +
libs/krypto/null-ncbi.c | 251 +
libs/krypto/null-ncbi.vec.pic.o.list | 4406 ++
libs/krypto/null-ncbi.vecreg.pic.o.list | 4406 ++
libs/krypto/reencfile.c | 1255 +
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libs/wgsxf/build_read_type.c | 113 +
libs/wgsxf/build_scaffold.c | 388 +
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tools/Makefile | 25 +-
tools/align-info/Makefile | 37 +-
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tools/bam-loader/Globals.h | 90 +
tools/bam-loader/KFileHelper.c | 142 +
tools/bam-loader/KFileHelper.h | 48 +
tools/bam-loader/KVPFile.c | 355 +
tools/bam-loader/KVPFile.h | 164 +
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tools/bam-loader/loader-imp.c | 2097 +
tools/bam-loader/loader-imp.h | 29 +
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tools/cg-load/factory-evidence-dnbs.h | 43 +
tools/cg-load/factory-evidence-intervals.c | 306 +
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tools/cg-load/factory-file.h | 43 +
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tools/cg-load/factory-reads.c | 261 +
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tools/cg-load/writer-algn.c | 775 +
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tools/cg-load/writer-evidence-dnbs.c | 227 +
tools/cg-load/writer-evidence-dnbs.h | 88 +
tools/cg-load/writer-evidence-intervals.c | 255 +
tools/cg-load/writer-evidence-intervals.h | 68 +
tools/cg-load/writer-seq.c | 135 +
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tools/fastq-loader/Makefile | 222 +
tools/fastq-loader/fastq-grammar.c | 2100 +
tools/fastq-loader/fastq-grammar.y | 294 +
tools/fastq-loader/fastq-lex.c | 2418 +
tools/fastq-loader/fastq-lex.l | 294 +
tools/fastq-loader/fastq-loader.c | 541 +
tools/fastq-loader/fastq-parse.h | 140 +
tools/fastq-loader/fastq-reader.c | 701 +
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tools/sra-dump/fasta_dump.c | 752 +
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tools/sra-dump/fastq-dump.vers | 2 +-
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tools/sra-dump/fastq.c | 3507 +-
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tools/sra-load/abi-load.vers | 2 +-
tools/sra-load/abi-load.vers.h | 1 -
tools/sra-load/absolid-fmt.c | 6 -
tools/sra-load/common-xml.c | 79 +-
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tools/sra-load/experiment-xml.c | 170 +-
tools/sra-load/experiment-xml.h | 1 -
tools/sra-load/fastq-fmt.c | 33 +-
tools/sra-load/fastq-load.vers | 2 +-
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tools/sra-load/illumina-fmt.c | 5 -
tools/sra-load/illumina-load.vers | 2 +-
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tools/sra-load/writer-absolid.c | 10 +-
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tools/sra-pileup/Makefile | 152 +
tools/sra-pileup/cg_tools.c | 532 +
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tools/sra-pileup/cmdline_cmn.c | 1042 +
tools/sra-pileup/cmdline_cmn.h | 133 +
tools/{sam-dump => sra-pileup}/debug.h | 0
tools/sra-pileup/inputfiles.c | 376 +
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tools/sra-pileup/matecache.c | 439 +
tools/sra-pileup/matecache.h | 119 +
tools/sra-pileup/out_redir.c | 120 +
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tools/sra-pileup/read_fkt.c | 338 +
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tools/sra-pileup/reref.c | 498 +
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tools/sra-pileup/sam-aligned.c | 1604 +
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tools/sra-pileup/sam-dump.c | 4917 ++
tools/sra-pileup/sam-dump.vers | 1 +
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tools/sra-stat/Makefile | 42 +-
tools/sra-stat/sra-stat.c | 2353 +-
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tools/srapath/Makefile | 96 +
tools/srapath/srapath.c | 283 +
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tools/util/Makefile | 131 +-
tools/util/kdbmeta.c | 545 +-
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tools/util/kdbmeta.vers.h | 1 -
tools/util/mac/syspass.c | 48 +
tools/util/rcexplain.vers | 2 +-
tools/util/rcexplain.vers.h | 1 -
tools/util/rowwritetest.c | 14 +-
tools/util/rowwritetest.vers | 2 +-
tools/util/syspass-priv.h | 44 +
tools/util/test-sra.c | 1165 +
tools/util/test-sra.vers | 1 +
tools/util/testld.vers | 2 +-
tools/util/txt2kdb.vers | 2 +-
tools/util/unix/syspass.c | 62 +
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tools/util/vdb-lock.vers | 2 +-
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tools/util/vdb-passwd.c | 276 +
tools/util/vdb-passwd.vers | 1 +
tools/util/vdb-unlock.c | 4 +-
tools/util/vdb-unlock.vers | 2 +-
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tools/util/win/syspass.c | 53 +
tools/vdb-config/Makefile | 25 +-
tools/vdb-config/vdb-config.c | 386 +-
tools/vdb-config/vdb-config.vers | 2 +-
tools/vdb-config/vdb-config.vers.h | 1 -
tools/vdb-copy/Makefile | 37 +-
tools/vdb-copy/coldefs.c | 43 +-
tools/vdb-copy/coldefs.h | 2 +-
tools/vdb-copy/context.c | 4 +
tools/vdb-copy/context.h | 8 +
tools/vdb-copy/copy_meta.c | 165 +-
tools/vdb-copy/definitions.h | 2 +
tools/vdb-copy/helper.c | 14 +-
tools/vdb-copy/helper.h | 3 +-
tools/vdb-copy/namelist_tools.c | 2 +-
tools/vdb-copy/num-gen.c | 10 +-
tools/vdb-copy/progressbar.c | 18 +-
tools/vdb-copy/redactval.c | 1 -
tools/vdb-copy/type_matcher.c | 24 +-
tools/vdb-copy/vdb-copy-includes.h | 2 +
tools/vdb-copy/vdb-copy.c | 119 +-
tools/vdb-copy/vdb-copy.vers | 2 +-
tools/vdb-copy/vdb-copy.vers.h | 1 -
tools/vdb-decrypt/Makefile | 130 +
tools/vdb-decrypt/shared.c | 1270 +
tools/vdb-decrypt/shared.h | 93 +
tools/vdb-decrypt/vdb-decrypt.c | 280 +
tools/vdb-decrypt/vdb-decrypt.vers | 1 +
tools/vdb-decrypt/vdb-encrypt.c | 227 +
tools/vdb-decrypt/vdb-encrypt.vers | 1 +
tools/vdb-dump/Makefile | 39 +-
tools/vdb-dump/vdb-dump-coldefs.c | 258 +-
tools/vdb-dump/vdb-dump-coldefs.h | 4 +-
tools/vdb-dump/vdb-dump-context.c | 79 +-
tools/vdb-dump/vdb-dump-context.h | 17 +-
tools/vdb-dump/vdb-dump-filter.c | 4 +-
tools/vdb-dump/vdb-dump-formats.c | 55 +-
tools/vdb-dump/vdb-dump-helper.c | 78 +-
tools/vdb-dump/vdb-dump-helper.h | 2 +-
tools/vdb-dump/vdb-dump-num-gen.c | 4 +-
tools/vdb-dump/vdb-dump-num-gen.h | 3 +-
tools/vdb-dump/vdb-dump-row-context.h | 1 +
tools/vdb-dump/vdb-dump-str.c | 32 +-
tools/vdb-dump/vdb-dump-tools.c | 1 -
tools/vdb-dump/vdb-dump.c | 767 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-dump/vdb-dump.vers.h | 1 -
tools/vdb-validate/Makefile | 114 +
tools/vdb-validate/vdb-validate.c | 2325 +
tools/vdb-validate/vdb-validate.vers | 1 +
1031 files changed, 456708 insertions(+), 20505 deletions(-)
delete mode 100644 CHANGES
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create mode 100644 interfaces/ext/libxml/parser.h
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create mode 100644 interfaces/ext/libxml/pattern.h
create mode 100644 interfaces/ext/libxml/relaxng.h
create mode 100644 interfaces/ext/libxml/schemasInternals.h
create mode 100644 interfaces/ext/libxml/schematron.h
create mode 100644 interfaces/ext/libxml/threads.h
create mode 100644 interfaces/ext/libxml/tree.h
create mode 100644 interfaces/ext/libxml/uri.h
create mode 100644 interfaces/ext/libxml/valid.h
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create mode 100644 interfaces/ext/libxml/xmlerror.h
create mode 100644 interfaces/ext/libxml/xmlexports.h
create mode 100644 interfaces/ext/libxml/xmlmemory.h
create mode 100644 interfaces/ext/libxml/xmlmodule.h
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create mode 100644 interfaces/ext/libxml/xmlschemastypes.h
create mode 100644 interfaces/ext/libxml/xmlstring.h
create mode 100644 interfaces/ext/libxml/xmlunicode.h
create mode 100644 interfaces/ext/libxml/xmlversion.h
create mode 100644 interfaces/ext/libxml/xmlwriter.h
create mode 100644 interfaces/ext/libxml/xpath.h
create mode 100644 interfaces/ext/libxml/xpathInternals.h
create mode 100644 interfaces/ext/libxml/xpointer.h
create mode 100644 interfaces/kapp/queue-file.h
create mode 100644 interfaces/kfg/repository.h
create mode 100644 interfaces/kfs/cacheteefile.h
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create mode 100644 interfaces/kfs/ramfile.h
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delete mode 100644 interfaces/klib/xml.h
delete mode 100644 interfaces/klib/xml.hpp
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create mode 100644 interfaces/kns/impl.h
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create mode 100644 interfaces/kns/stream.h
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create mode 100644 interfaces/kproc/timeout.h
create mode 100644 interfaces/krypto/cipher-impl.h
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create mode 100644 interfaces/krypto/rng-impl.h
create mode 100644 interfaces/krypto/rng.h
create mode 100644 interfaces/krypto/testciphermgr.h
create mode 100644 interfaces/krypto/wgaencrypt.h
create mode 100644 interfaces/kxml/xml.h
create mode 100644 interfaces/loader/alignment-writer.h
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create mode 100644 interfaces/loader/reference-writer.h
create mode 100644 interfaces/loader/sequence-writer.h
create mode 100644 interfaces/ncbi/wgs-contig.h
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create mode 100644 libs/align/pl_iterator.c
create mode 100644 libs/align/quality-quantizer.c
create mode 100644 libs/align/ref_iterator.c
create mode 100644 libs/align/reference-cmn.c
create mode 100644 libs/align/reference-cmn.h
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create mode 100644 libs/axf/ref-tbl.h
create mode 100644 libs/axf/seq-construct-read.c
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create mode 100644 libs/kfg/report.c
create mode 100644 libs/kfg/repository.c
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create mode 100644 libs/klib/judy/JudyPrintJP.c
create mode 100644 libs/klib/judy/JudyPrivate.h
create mode 100644 libs/klib/judy/JudyPrivate1L.h
create mode 100644 libs/klib/judy/JudyPrivateBranch.h
create mode 100644 libs/klib/judy/JudySL.c
create mode 100644 libs/klib/judy/JudyTablesGen.c
create mode 100644 libs/klib/judy/Makefile
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create mode 100644 libs/kns/KCurlFile.c
create mode 100644 libs/kns/KCurlRequest.c
create mode 100644 libs/kns/Makefile
create mode 100644 libs/kns/curlhdr/curl.h
create mode 100644 libs/kns/curlhdr/curlver.h
create mode 100644 libs/kns/curlhdr/easy.h
create mode 100644 libs/kns/curlhdr/multi.h
create mode 100644 libs/kns/curlhdr/types.h
create mode 100644 libs/kns/entrez-fetcher.c
create mode 100644 libs/kns/kns_manager.c
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create mode 100644 libs/kns/libkurl.vers
create mode 100644 libs/kns/stream-from-files.c
create mode 100644 libs/kns/stream-from-streams.c
create mode 100644 libs/kns/stream-priv.h
create mode 100644 libs/kns/stream.c
create mode 100644 libs/kns/url-fetcher-curl.c
create mode 100644 libs/kns/url-fetcher-impl.h
create mode 100644 libs/kns/url-fetcher.c
create mode 100644 libs/kproc/procmgr.c
create mode 100644 libs/kproc/task.c
create mode 100644 libs/krypto/Makefile
create mode 100644 libs/krypto/aes-byte.c
create mode 100644 libs/krypto/aes-ncbi-priv.h
create mode 100644 libs/krypto/aes-ncbi.aes-ni.pic.o.list
create mode 100644 libs/krypto/aes-ncbi.c
create mode 100644 libs/krypto/aes-ncbi.vec.pic.o.list
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create mode 100644 libs/krypto/aes-priv.h
create mode 100644 libs/krypto/aes.c
create mode 100644 libs/krypto/aes_core.c
create mode 100644 libs/krypto/blockcipher-impl.h
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create mode 100644 libs/krypto/cipher-impl.h
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create mode 100644 libs/krypto/cipher-vec.vec.pic.o.list
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create mode 100644 libs/krypto/manager.c
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create mode 100644 libs/krypto/reencfile.c
create mode 100644 libs/krypto/rng-impl.h
rename build/STATIC => libs/krypto/rng-priv.h (100%)
create mode 100644 libs/krypto/rng.c
create mode 100644 libs/krypto/testcipher.c
create mode 100644 libs/krypto/wgaencrypt.c
create mode 100644 libs/ktst/Makefile
create mode 100644 libs/ktst/testcase.cpp
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create mode 100644 libs/ktst/unix/runprocesstestcase.cpp
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create mode 100644 libs/loader/Makefile
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create mode 100644 libs/wgsxf/build_scaffold.c
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rename libs/{align/libalign-writer.vers => wgsxf/libwwgsxf.vers} (100%)
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create mode 100644 tools/bam-loader/KFileHelper.h
create mode 100644 tools/bam-loader/KVPFile.c
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