[Debian-med-packaging] Please test sra-toolkit (Was: 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)
Andreas Tille
andreas at an3as.eu
Tue Aug 13 19:30:43 UTC 2013
Hi,
I realised that updating sra-sdk is way more work than expected but I
got some testable state into the new Git repository. I wonder whether
anybody could give it a try to make sure I will only have broken the
repository and not even messed up with the whole package. It needs to
be a severy cleaning up of lintian issues and I might do this the day
after tomorrow but if somebody meanwhile could do some testing that
would be welcome.
Kind regards
Andreas.
On Tue, Aug 13, 2013 at 03:51:03PM +0200, Andreas Tille wrote:
> 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 +
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> 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 +-
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> interfaces/kdb/database.h | 18 +-
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> interfaces/kfs/arc.h | 14 +
> interfaces/kfs/buffile.h | 10 +
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> interfaces/kfs/directory.h | 63 +-
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> interfaces/kfs/lockfile.h | 116 +
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> 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 +-
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> interfaces/klib/klib-priv.h | 106 +
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> 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 +
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> 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 +-
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> 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 +
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> libs/kdb/colidx2.c | 114 +-
> libs/kdb/column-cc.c | 67 +-
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> libs/kdb/database-cc.c | 232 +-
> libs/kdb/database-cmn.c | 2 +-
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> libs/kdb/dbmgr.c | 255 +-
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> 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 +-
> libs/klib/win/syserrcode.c | 2 +-
> libs/klib/win/syswriter.c | 17 +-
> libs/klib/writer.c | 8 +-
> libs/kns/KCurlFile.c | 716 +
> libs/kns/KCurlRequest.c | 438 +
> libs/kns/Makefile | 125 +
> libs/kns/curlhdr/curl.h | 1600 +
> libs/kns/curlhdr/curlver.h | 56 +
> libs/kns/curlhdr/easy.h | 81 +
> libs/kns/curlhdr/multi.h | 344 +
> libs/kns/curlhdr/types.h | 1 +
> libs/kns/entrez-fetcher.c | 221 +
> libs/kns/kns_manager.c | 263 +
> libs/kns/kns_mgr_priv.h | 59 +
> .../libalign-writer.vers => kns/libkns.vers} | 0
> libs/kns/libkurl.vers | 1 +
> libs/kns/stream-from-files.c | 168 +
> libs/kns/stream-from-streams.c | 150 +
> libs/kns/stream-priv.h | 32 +
> libs/kns/stream.c | 336 +
> libs/kns/url-fetcher-curl.c | 255 +
> libs/kns/url-fetcher-impl.h | 109 +
> libs/kns/url-fetcher.c | 129 +
> libs/kproc/Makefile | 55 +-
> libs/kproc/bsd/syslock.c | 1 +
> libs/kproc/libkproc.vers | 2 +-
> libs/kproc/libkq.vers | 2 +-
> libs/kproc/libksproc.vers | 2 +-
> libs/kproc/linux/syslock.c | 1 +
> libs/kproc/procmgr.c | 412 +
> libs/kproc/queue.c | 93 +-
> libs/kproc/sem.c | 79 +-
> libs/kproc/sttimeout.c | 1 +
> libs/kproc/task.c | 156 +
> libs/kproc/unix/syscond.c | 46 +-
> libs/kproc/unix/systimeout.c | 1 +
> libs/kproc/win/syscond-priv.h | 10 +-
> libs/kproc/win/syscond.c | 238 +-
> libs/kproc/win/syslock.c | 6 +-
> libs/krypto/Makefile | 336 +
> libs/krypto/aes-byte.c | 236 +
> libs/krypto/aes-ncbi-priv.h | 227 +
> libs/krypto/aes-ncbi.aes-ni.pic.o.list |38295 ++++++++++
> libs/krypto/aes-ncbi.c | 2644 +
> libs/krypto/aes-ncbi.vec.pic.o.list |74023 +++++++++++++++++++
> libs/krypto/aes-ncbi.vecreg.pic.o.list |75192 ++++++++++++++++++++
> libs/krypto/aes-priv.h | 94 +
> libs/krypto/aes.c | 1 +
> libs/krypto/aes_core.c | 1181 +
> libs/krypto/blockcipher-impl.h | 187 +
> libs/krypto/blockcipher-priv.h | 90 +
> libs/krypto/blockcipher.c | 3 +
> libs/krypto/cipher-byte.c | 522 +
> libs/krypto/cipher-impl.h | 174 +
> libs/krypto/cipher-no-vec.c | 41 +
> 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 +++
> libs/krypto/cipher.c | 536 +
> libs/krypto/ciphermgr.c | 295 +
> libs/krypto/compile-test.aes-ni.pic.o.list | 592 +
> libs/krypto/compile-test.c | 50 +
> libs/krypto/compile-test.vec.pic.o.list | 590 +
> libs/krypto/compile-test.vecreg.pic.o.list | 592 +
> libs/krypto/csprng.c | 163 +
> libs/krypto/encfile-priv.h | 163 +
> libs/krypto/encfile.c | 2122 +
> libs/krypto/encfilev2.c | 2589 +
> libs/krypto/key.c | 126 +
> libs/krypto/libkrypto.vers | 1 +
> .../libkryptotest.vers} | 0
> libs/krypto/manager.c | 11 +
> libs/krypto/ncbi-priv.h | 122 +
> libs/krypto/no-null-ncbi.aes-ni.pic.o.list | 2539 +
> libs/krypto/no-null-ncbi.c | 59 +
> libs/krypto/no-null-ncbi.vec.pic.o.list | 2540 +
> libs/krypto/no-null-ncbi.vecreg.pic.o.list | 2540 +
> 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 +
> libs/krypto/rng-impl.h | 91 +
> build/STATIC => libs/krypto/rng-priv.h | 0
> libs/krypto/rng.c | 120 +
> libs/krypto/testcipher.c | 76 +
> libs/krypto/wgaencrypt.c | 1254 +
> libs/ktst/Makefile | 90 +
> libs/ktst/testcase.cpp | 95 +
> libs/ktst/testenv.cpp | 503 +
> libs/ktst/testrunner.cpp | 77 +
> libs/ktst/unix/runprocesstestcase.cpp | 100 +
> libs/ktst/win/runprocesstestcase.cpp | 141 +
> libs/kxml/Makefile | 4 +-
> libs/kxml/libkxfs.vers | 2 +-
> libs/kxml/libkxml.vers | 2 +-
> libs/kxml/xml.c | 44 +-
> libs/kxml/xtoc-parsexml.c | 36 +-
> libs/kxml/xtoc.c | 389 +-
> libs/loader/Makefile | 99 +
> libs/loader/alignment-writer.c | 226 +
> libs/loader/common-reader.c | 614 +
> libs/loader/common-writer.c | 1987 +
> libs/loader/mmarray.c | 131 +
> libs/loader/reference-writer.c | 459 +
> libs/loader/sequence-writer.c | 361 +
> libs/search/Makefile | 10 +-
> libs/search/libksrch.vers | 2 +-
> libs/search/libksrch.vers.h | 1 -
> libs/sra/Makefile | 99 +-
> libs/sra/libsradb.vers | 2 +-
> libs/sra/libsradb.vers.h | 1 -
> libs/sra/libsrareader.vers | 2 +-
> libs/sra/libsrareader.vers.h | 1 -
> libs/sra/libsraschema.vers.h | 1 -
> libs/sra/libwsradb.vers | 2 +-
> libs/sra/libwsradb.vers.h | 1 -
> libs/sra/libwsraschema.vers.h | 1 -
> libs/sra/reader-abi.c | 25 +-
> libs/sra/reader-fastq.c | 16 +-
> libs/sra/reader-illumina.c | 96 +-
> libs/sra/reader-sff.c | 115 +-
> libs/sra/sra-dflt-schema.c | 1 -
> libs/sra/sra-priv.h | 21 +-
> libs/sra/sracache.c | 466 +
> libs/sra/sramgr-cmn.c | 206 +-
> libs/sra/srapath-stub.c | 408 -
> libs/sra/sraschema-stub.c | 67 -
> libs/sra/sratbl-cmn.c | 320 +-
> libs/sra/wsramgr.c | 1 +
> libs/sra/wsraschema-stub.c | 67 -
> libs/sra/wsratbl.c | 19 +-
> libs/sraxf/Makefile | 26 +-
> libs/sraxf/fix_read_seg_impl.h | 169 +
> libs/sraxf/format-spot-name.c | 11 +-
> libs/sraxf/index_lookup.c | 23 +-
> libs/sraxf/libsraxf.vers | 2 +-
> libs/sraxf/libsraxf.vers.h | 1 -
> libs/sraxf/libwsraxf.vers | 2 +-
> libs/sraxf/libwsraxf.vers.h | 1 -
> libs/sraxf/prefix-tree-to-name.c | 2 -
> libs/sraxf/read-desc.c | 9 +-
> libs/sraxf/read-seg-from-readn.c | 43 +-
> libs/sraxf/stats.c | 193 +-
> libs/sraxf/stats_quality.c | 2 +-
> libs/sraxf/tokenize-spot_name-ion-torrent.c | 67 +-
> libs/vdb/Makefile | 25 +-
> libs/vdb/blob-priv.h | 67 +-
> libs/vdb/blob.c | 895 +-
> libs/vdb/blob.h | 7 -
> libs/vdb/column-cmn.c | 22 +-
> libs/vdb/column-priv.h | 56 +-
> libs/vdb/cursor-cmn.c | 656 +-
> libs/vdb/cursor-priv.h | 36 +-
> libs/vdb/cursor.c | 3 +-
> libs/vdb/database-cmn.c | 25 +
> libs/vdb/database-depend.c | 1715 +
> libs/vdb/dbmgr-cmn.c | 324 +-
> libs/vdb/dbmgr-priv.h | 42 -
> libs/vdb/dbmgr.c | 5 -
> libs/vdb/delta_average.c | 297 +
> libs/vdb/libvdb.vers | 2 +-
> libs/vdb/libvdb.vers.h | 1 -
> libs/vdb/libwvdb.vers | 2 +-
> libs/vdb/libwvdb.vers.h | 1 -
> libs/vdb/linker-cmn.c | 25 +
> libs/vdb/linker-int.c | 11 +-
> libs/vdb/linker-priv.h | 7 +
> libs/vdb/meta-attr-write.c | 21 +-
> libs/vdb/page-map.c | 1397 +-
> libs/vdb/page-map.h | 291 +-
> libs/vdb/phys-cmn.c | 39 +-
> libs/vdb/prod-cmn.c | 291 +-
> libs/vdb/prod-expr.c | 12 +-
> libs/vdb/prod-func.c | 6 +-
> libs/vdb/prod-priv.h | 50 +-
> libs/vdb/prod.c | 13 +
> libs/vdb/redimension.c | 1 +
> libs/vdb/report-vdb.c | 856 +
> libs/vdb/schema-dump.c | 37 +-
> libs/vdb/schema-expr.c | 11 +-
> libs/vdb/schema-int.c | 1 +
> libs/vdb/schema-parse.c | 8 +
> libs/vdb/schema-parse.h | 5 +
> libs/vdb/schema-priv.h | 3 +
> libs/vdb/schema-tbl.c | 54 +-
> libs/vdb/schema-type.c | 18 +-
> libs/vdb/schema.c | 26 +-
> libs/vdb/table-cmn.c | 123 +-
> libs/vdb/table-priv.h | 2 +-
> libs/vdb/wcolumn.c | 1177 +-
> libs/vdb/wcursor.c | 274 +-
> libs/vdb/wdbmgr.c | 7 -
> libs/vdb/wphys.c | 99 +-
> libs/vdb/wprod.c | 28 +-
> libs/vdb/wtable.c | 113 +-
> libs/vfs/Makefile | 139 +
> libs/vfs/libsrapath.vers | 1 +
> libs/vfs/libvfs.vers | 1 +
> libs/vfs/manager.c | 3709 +
> libs/vfs/path-priv.h | 115 +
> libs/vfs/path.c | 2457 +
> libs/vfs/resolver-priv.h | 144 +
> libs/vfs/resolver.c | 2694 +
> libs/vfs/srapath-stub.c | 372 +
> libs/vfs/srapath.c | 1424 +
> libs/vfs/unix/syspath.c | 127 +
> libs/vfs/win/syspath.c | 288 +
> libs/vxf/Makefile | 68 +-
> libs/vxf/checksum.c | 2 +
> libs/vxf/irzip.c | 6 +-
> libs/vxf/irzip.impl.h | 174 +-
> libs/vxf/iunzip.c | 7 +-
> libs/vxf/izip-common.h | 4 +-
> libs/vxf/libvxf.vers | 2 +-
> libs/vxf/libvxf.vers.h | 1 -
> libs/vxf/libwvxf.vers | 2 +-
> libs/vxf/lower-case-tech-reads.c | 111 +
> libs/vxf/math-funcs-impl.h | 2 +-
> libs/vxf/simple-sub-select.c | 79 +-
> libs/vxf/sprintf.c | 1308 +-
> libs/vxf/unzip.c | 16 +-
> libs/vxf/vec-sum.c | 214 +-
> libs/vxf/wgs-tokenize-accession.c | 212 +
> libs/wgsxf/Makefile | 138 +
> libs/wgsxf/build_read_type.c | 113 +
> libs/wgsxf/build_scaffold.c | 388 +
> .../libalign-writer.vers => wgsxf/libwgsxf.vers} | 0
> .../libalign-writer.vers => wgsxf/libwwgsxf.vers} | 0
> tools/Makefile | 25 +-
> tools/align-info/Makefile | 37 +-
> tools/align-info/align-info.c | 547 +-
> tools/align-info/align-info.vers | 2 +-
> tools/align-info/align-info.vers.h | 1 -
> 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 +
> tools/bam-loader/Makefile | 136 +
> tools/bam-loader/alignment-writer.c | 176 +
> tools/bam-loader/alignment-writer.h | 95 +
> tools/bam-loader/analysis.c | 157 +
> tools/bam-loader/analysis.h | 49 +
> tools/bam-loader/bam-load.vers | 1 +
> tools/bam-loader/bam-loader.c | 987 +
> tools/bam-loader/hashtable.c | 878 +
> tools/bam-loader/hashtable.h | 55 +
> tools/bam-loader/loader-imp.c | 2097 +
> tools/bam-loader/loader-imp.h | 29 +
> tools/bam-loader/reference-writer.c | 447 +
> tools/bam-loader/reference-writer.h | 69 +
> tools/bam-loader/sequence-writer.c | 345 +
> tools/bam-loader/sequence-writer.h | 84 +
> tools/cg-load/Makefile | 119 +
> tools/cg-load/cg-load.c | 1120 +
> tools/cg-load/cg-load.vers | 1 +
> tools/cg-load/debug.h | 34 +
> tools/cg-load/defs.h | 136 +
> tools/cg-load/f1_3.c | 76 +
> tools/cg-load/f1_5.c | 76 +
> tools/cg-load/f2_0.c | 79 +
> tools/cg-load/f2_2.c | 95 +
> tools/cg-load/factory-cmn.h | 61 +
> tools/cg-load/factory-evidence-dnbs.c | 351 +
> tools/cg-load/factory-evidence-dnbs.h | 43 +
> tools/cg-load/factory-evidence-intervals.c | 306 +
> tools/cg-load/factory-evidence-intervals.h | 43 +
> tools/cg-load/factory-file.h | 43 +
> tools/cg-load/factory-mappings.c | 338 +
> tools/cg-load/factory-mappings.h | 43 +
> tools/cg-load/factory-reads.c | 261 +
> tools/cg-load/factory-reads.h | 43 +
> tools/cg-load/file-version-factory.c | 157 +
> tools/cg-load/file.c | 403 +
> tools/cg-load/file.h | 330 +
> tools/cg-load/writer-algn.c | 775 +
> tools/cg-load/writer-algn.h | 62 +
> 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 +
> tools/cg-load/writer-seq.h | 58 +
> 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 +
> tools/fastq-loader/fastq-reader.h | 50 +
> tools/fastq-loader/fastq-tokens.h | 64 +
> tools/fastq-loader/latf-load.vers | 1 +
> tools/fastq-loader/loader-imp.c | 242 +
> tools/kar/Makefile | 34 +-
> tools/kar/kar.c | 104 +-
> tools/kar/kar.vers | 2 +-
> tools/kar/kar.vers.h | 1 -
> tools/kar/sra-kar.c | 37 +-
> tools/kar/sra-kar.vers | 2 +-
> tools/kar/sra-kar.vers.h | 1 -
> tools/nenctool/Makefile | 123 +
> tools/nenctool/nenctest.c | 502 +
> tools/nenctool/nenctest.vers | 1 +
> tools/nenctool/nenctool.c | 446 +
> tools/nenctool/nenctool.vers | 1 +
> tools/nencvalid/Makefile | 111 +
> tools/nencvalid/nencvalid.c | 683 +
> tools/nencvalid/nencvalid.vers | 1 +
> tools/prefetch/Makefile | 111 +
> tools/prefetch/prefetch.c | 1177 +
> tools/prefetch/prefetch.vers | 1 +
> tools/refseq-load/Makefile | 26 +-
> tools/refseq-load/context.c | 115 +-
> tools/refseq-load/context.h | 8 +-
> tools/refseq-load/definitions.h | 4 -
> tools/refseq-load/refseq-load.c | 468 +-
> tools/refseq-load/refseq-load.vers | 2 +-
> tools/refseq-load/refseq-load.vers.h | 1 -
> tools/sam-dump/Makefile | 38 +-
> tools/sam-dump/sam-dump.c | 5607 +-
> tools/sam-dump/sam-dump.vers | 2 +-
> tools/sam-dump/sam-dump.vers.h | 1 -
> tools/sra-dbcc/Makefile | 40 +-
> tools/sra-dbcc/sra-dbcc.c | 1464 +-
> tools/sra-dbcc/sra-dbcc.vers | 2 +-
> tools/sra-dbcc/sra-dbcc.vers.h | 1 -
> tools/sra-dump/Makefile | 46 +-
> tools/sra-dump/abi-dump.vers | 2 +-
> tools/sra-dump/abi-dump.vers.h | 1 -
> tools/sra-dump/abi.c | 118 +-
> tools/sra-dump/core.c | 1454 +-
> tools/sra-dump/core.h | 2 +-
> tools/sra-dump/factory.c | 77 +-
> tools/sra-dump/factory.h | 23 +-
> tools/sra-dump/fasta_dump.c | 752 +
> tools/sra-dump/fasta_dump.h | 36 +
> tools/sra-dump/fastq-dump.vers | 2 +-
> tools/sra-dump/fastq-dump.vers.h | 1 -
> tools/sra-dump/fastq.c | 3507 +-
> tools/sra-dump/illumina-dump.vers | 2 +-
> tools/sra-dump/illumina-dump.vers.h | 1 -
> tools/sra-dump/illumina.c | 110 +-
> tools/sra-dump/sff-dump.vers | 2 +-
> tools/sra-dump/sff-dump.vers.h | 1 -
> tools/sra-dump/sff.c | 23 +-
> tools/sra-dump/sra-dump.c | 60 +-
> tools/sra-dump/sra-dump.vers | 2 +-
> tools/sra-dump/sra-dump.vers.h | 1 -
> tools/sra-load/Makefile | 36 +-
> 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 +-
> tools/sra-load/common-xml.h | 30 +-
> 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 +-
> tools/sra-load/fastq-load.vers.h | 1 -
> tools/sra-load/helicos-fmt.c | 5 -
> tools/sra-load/helicos-load.vers | 2 +-
> tools/sra-load/helicos-load.vers.h | 1 -
> tools/sra-load/illumina-fmt.c | 5 -
> tools/sra-load/illumina-load.vers | 2 +-
> tools/sra-load/illumina-load.vers.h | 1 -
> tools/sra-load/loader-file.c | 9 +-
> tools/sra-load/loader-file.h | 4 +-
> tools/sra-load/loader-fmt.h | 1 +
> tools/sra-load/loader.c | 66 +-
> tools/sra-load/run-xml.c | 5 +-
> tools/sra-load/run-xml.h | 3 +-
> tools/sra-load/sff-fmt.c | 5 -
> tools/sra-load/sff-load.vers | 2 +-
> tools/sra-load/sff-load.vers.h | 1 -
> tools/sra-load/srf-fmt.c | 5 -
> tools/sra-load/srf-load.vers | 2 +-
> tools/sra-load/srf-load.vers.h | 1 -
> tools/sra-load/writer-absolid.c | 10 +-
> tools/sra-load/writer-absolid.h | 5 +-
> tools/sra-pileup/Makefile | 152 +
> tools/sra-pileup/cg_tools.c | 532 +
> tools/sra-pileup/cg_tools.h | 64 +
> 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 +
> tools/sra-pileup/inputfiles.h | 99 +
> tools/sra-pileup/matecache.c | 439 +
> tools/sra-pileup/matecache.h | 119 +
> tools/sra-pileup/out_redir.c | 120 +
> tools/sra-pileup/out_redir.h | 64 +
> tools/sra-pileup/read_fkt.c | 338 +
> tools/sra-pileup/read_fkt.h | 63 +
> tools/sra-pileup/reref.c | 498 +
> tools/sra-pileup/reref.h | 48 +
> tools/sra-pileup/sam-aligned.c | 1604 +
> tools/sra-pileup/sam-aligned.h | 45 +
> tools/sra-pileup/sam-dump-opts.c | 1493 +
> tools/sra-pileup/sam-dump-opts.h | 277 +
> tools/sra-pileup/sam-dump.c | 4917 ++
> tools/sra-pileup/sam-dump.vers | 1 +
> tools/sra-pileup/sam-dump3.c | 532 +
> tools/sra-pileup/sam-hdr.c | 425 +
> tools/sra-pileup/sam-hdr.h | 41 +
> tools/sra-pileup/sam-unaligned.c | 1411 +
> tools/sra-pileup/sam-unaligned.h | 43 +
> tools/sra-pileup/sra-pileup.c | 1834 +
> tools/sra-pileup/sra-pileup.vers | 1 +
> tools/sra-sort/Makefile | 141 +
> tools/sra-sort/Makefile.cc | 24 +
> tools/sra-sort/Makefile.clang | 27 +
> tools/sra-sort/Makefile.gcc | 27 +
> tools/sra-sort/Makefile.vc++ | 24 +
> tools/sra-sort/buff-writer.c | 785 +
> 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 | 816 +
> tools/sra-sort/col-pair.h | 323 +
> tools/sra-sort/csra-pair.c | 216 +
> tools/sra-sort/csra-pair.h | 84 +
> tools/sra-sort/csra-tbl.c | 783 +
> tools/sra-sort/csra-tbl.h | 83 +
> tools/sra-sort/ctx.h | 105 +
> tools/sra-sort/db-pair.c | 883 +
> tools/sra-sort/db-pair.h | 208 +
> tools/sra-sort/dir-pair.c | 504 +
> tools/sra-sort/dir-pair.h | 124 +
> tools/sra-sort/dump-blob-boundaries.c | 203 +
> tools/sra-sort/except.c | 231 +
> tools/sra-sort/except.h | 160 +
> tools/sra-sort/gcc-ped.sh | 39 +
> tools/sra-sort/glob-poslen.c | 349 +
> tools/sra-sort/glob-poslen.h | 95 +
> tools/sra-sort/id-mapper-col.c | 260 +
> tools/sra-sort/id-mapper-col.h | 55 +
> tools/sra-sort/idx-mapping.c | 92 +
> 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 | 705 +
> 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 | 82 +
> tools/sra-sort/sorting-row-set.c | 405 +
> tools/sra-sort/sra-sort.c | 754 +
> tools/sra-sort/sra-sort.h | 171 +
> tools/sra-sort/sra-sort.vers | 1 +
> tools/sra-sort/status.h | 48 +
> tools/sra-sort/tbl-pair.c | 1055 +
> tools/sra-sort/tbl-pair.h | 209 +
> tools/sra-sort/xcheck-ref-align.c | 404 +
> tools/sra-sort/xcheck.h | 49 +
> tools/sra-stat/Makefile | 42 +-
> tools/sra-stat/sra-stat.c | 2353 +-
> tools/sra-stat/sra-stat.vers | 2 +-
> tools/sra-stat/sra-stat.vers.h | 1 -
> tools/srapath/Makefile | 96 +
> tools/srapath/srapath.c | 283 +
> tools/srapath/srapath.vers | 1 +
> tools/util/Makefile | 131 +-
> tools/util/kdbmeta.c | 545 +-
> tools/util/kdbmeta.vers | 2 +-
> 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 +
> tools/util/vdb-lock.c | 4 +-
> tools/util/vdb-lock.vers | 2 +-
> tools/util/vdb-lock.vers.h | 1 -
> tools/util/vdb-passwd.c | 276 +
> tools/util/vdb-passwd.vers | 1 +
> tools/util/vdb-unlock.c | 4 +-
> tools/util/vdb-unlock.vers | 2 +-
> tools/util/vdb-unlock.vers.h | 1 -
> 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
> delete mode 100644 README-build
> create mode 100644 README-build.txt
> create mode 100644 README-config.txt
> delete mode 100644 USAGE
> create mode 100644 build/LNKG.linux
> create mode 100644 build/LNKG.mac
> create mode 100644 build/LNKG.win
> create mode 100644 build/Makefile.clang
> create mode 100644 doc/help/html/bam-load-help.html
> delete mode 100644 doc/help/html/bam-loader-help.html
> mode change 100755 => 100644 doc/help/txt/fastq-dump-help.txt
> delete mode 100644 interfaces/align/alignarc.h
> create mode 100644 interfaces/align/dna-reverse-cmpl.h
> create mode 100644 interfaces/align/iterator.h
> create mode 100644 interfaces/align/manager.h
> create mode 100644 interfaces/align/qstat.vschema
> create mode 100644 interfaces/align/quality-quantizer.h
> create mode 100644 interfaces/align/reference.h
> create mode 100644 interfaces/align/refseq.vschema
> create mode 100644 interfaces/align/seq.vschema
> delete mode 100644 interfaces/cc/gcc/i386/fmtdef.h
> create mode 100644 interfaces/cc/gcc/v128.h
> delete mode 100644 interfaces/cc/gcc/x86_64/fmtdef.h
> delete mode 100644 interfaces/cc/vc++/i386/fmtdef.h
> delete mode 100644 interfaces/cc/vc++/x86_64/fmtdef.h
> create mode 100644 interfaces/ext/libxml/DOCBparser.h
> create mode 100644 interfaces/ext/libxml/HTMLparser.h
> create mode 100644 interfaces/ext/libxml/HTMLtree.h
> create mode 100644 interfaces/ext/libxml/SAX.h
> create mode 100644 interfaces/ext/libxml/SAX2.h
> create mode 100644 interfaces/ext/libxml/c14n.h
> create mode 100644 interfaces/ext/libxml/catalog.h
> create mode 100644 interfaces/ext/libxml/chvalid.h
> create mode 100644 interfaces/ext/libxml/debugXML.h
> create mode 100644 interfaces/ext/libxml/dict.h
> create mode 100644 interfaces/ext/libxml/encoding.h
> create mode 100644 interfaces/ext/libxml/entities.h
> create mode 100644 interfaces/ext/libxml/globals.h
> create mode 100644 interfaces/ext/libxml/hash.h
> create mode 100644 interfaces/ext/libxml/list.h
> create mode 100644 interfaces/ext/libxml/nanoftp.h
> create mode 100644 interfaces/ext/libxml/nanohttp.h
> create mode 100644 interfaces/ext/libxml/parser.h
> create mode 100644 interfaces/ext/libxml/parserInternals.h
> 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
> create mode 100644 interfaces/ext/libxml/xinclude.h
> create mode 100644 interfaces/ext/libxml/xlink.h
> create mode 100644 interfaces/ext/libxml/xmlIO.h
> create mode 100644 interfaces/ext/libxml/xmlautomata.h
> 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
> create mode 100644 interfaces/ext/libxml/xmlreader.h
> create mode 100644 interfaces/ext/libxml/xmlregexp.h
> create mode 100644 interfaces/ext/libxml/xmlsave.h
> create mode 100644 interfaces/ext/libxml/xmlschemas.h
> 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
> create mode 100644 interfaces/kfs/lockfile.h
> delete mode 100644 interfaces/kfs/path-priv.h
> delete mode 100644 interfaces/kfs/path.h
> create mode 100644 interfaces/kfs/quickmount.h
> create mode 100644 interfaces/kfs/ramfile.h
> create mode 100644 interfaces/kfs/readheadfile.h
> create mode 100644 interfaces/klib/klib-priv.h
> create mode 100644 interfaces/klib/ksort-macro.h
> create mode 100644 interfaces/klib/report.h
> delete mode 100644 interfaces/klib/xml.h
> delete mode 100644 interfaces/klib/xml.hpp
> create mode 100644 interfaces/kns/KCurlRequest.h
> create mode 100644 interfaces/kns/curl-file.h
> create mode 100644 interfaces/kns/entrez-fetcher.h
> create mode 100644 interfaces/kns/extern.h
> create mode 100644 interfaces/kns/impl.h
> create mode 100644 interfaces/kns/manager.h
> create mode 100644 interfaces/kns/stream.h
> create mode 100644 interfaces/kns/url-fetcher.h
> create mode 100644 interfaces/kproc/impl.h
> create mode 100644 interfaces/kproc/procmgr.h
> create mode 100644 interfaces/kproc/task.h
> create mode 100644 interfaces/kproc/timeout.h
> create mode 100644 interfaces/krypto/cipher-impl.h
> create mode 100644 interfaces/krypto/cipher-priv.h
> create mode 100644 interfaces/krypto/cipher-test.h
> create mode 100644 interfaces/krypto/cipher.h
> create mode 100644 interfaces/krypto/ciphermgr-priv.h
> create mode 100644 interfaces/krypto/ciphermgr.h
> create mode 100644 interfaces/krypto/encfile-priv.h
> create mode 100644 interfaces/krypto/encfile.h
> create mode 100644 interfaces/krypto/extern.h
> create mode 100644 interfaces/krypto/key.h
> create mode 100644 interfaces/krypto/manager-priv.h
> create mode 100644 interfaces/krypto/manager.h
> create mode 100644 interfaces/krypto/reencfile.h
> 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
> create mode 100644 interfaces/loader/common-reader-priv.h
> create mode 100644 interfaces/loader/common-reader.h
> create mode 100644 interfaces/loader/common-writer.h
> create mode 100644 interfaces/loader/mmarray.h
> create mode 100644 interfaces/loader/reference-writer.h
> create mode 100644 interfaces/loader/sequence-writer.h
> create mode 100644 interfaces/ncbi/wgs-contig.h
> create mode 100644 interfaces/ncbi/wgs-contig.vschema
> create mode 100644 interfaces/vdb/blob.h
> create mode 100644 interfaces/vdb/dependencies.h
> create mode 100644 interfaces/vdb/report.h
> create mode 100644 interfaces/vfs/extern.h
> create mode 100644 interfaces/vfs/manager-priv.h
> create mode 100644 interfaces/vfs/manager.h
> create mode 100644 interfaces/vfs/path-priv.h
> create mode 100644 interfaces/vfs/path.h
> create mode 100644 interfaces/vfs/resolver.h
> create mode 100644 libs/align/al_iterator.c
> create mode 100644 libs/align/align_mgr.c
> create mode 100644 libs/align/dna-reverse-cmpl.c
> 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
> create mode 100644 libs/align/reference.c
> create mode 100644 libs/axf/get_mate_align_ids.c
> delete mode 100644 libs/axf/libaxf.vers.h
> delete mode 100644 libs/axf/libwaxf.vers.h
> create mode 100644 libs/axf/make-cmp-read_desc.c
> create mode 100644 libs/axf/ref-tbl.c
> create mode 100644 libs/axf/ref-tbl.h
> create mode 100644 libs/axf/seq-construct-read.c
> delete mode 100644 libs/ext/Makefile
> delete mode 100644 libs/ext/bzip2/Makefile
> delete mode 100644 libs/ext/zlib/Makefile
> create mode 100644 libs/kapp/args_debug.h
> create mode 100644 libs/kapp/queue-file.c
> create mode 100644 libs/kapp/tokenizer.c
> delete mode 100644 libs/kdb/libkdb.vers.h
> delete mode 100644 libs/kdb/libwkdb.vers.h
> create mode 100644 libs/kfg/config-grammar.c
> create mode 100644 libs/kfg/config-lex.c
> create mode 100644 libs/kfg/config-tokens.h
> delete mode 100644 libs/kfg/config.linux.kfg
> delete mode 100644 libs/kfg/config.mac.kfg
> delete mode 100644 libs/kfg/config.win.kfg
> create mode 100644 libs/kfg/default.kfg
> create mode 100644 libs/kfg/kfg-parse.h
> create mode 100644 libs/kfg/report-kfg.c
> create mode 100644 libs/kfg/report.c
> create mode 100644 libs/kfg/repository.c
> create mode 100644 libs/kfs/buffile-read.c
> create mode 100644 libs/kfs/cacheteefile.c
> create mode 100644 libs/kfs/lockfile.c
> delete mode 100644 libs/kfs/path-priv.h
> delete mode 100644 libs/kfs/path.c
> create mode 100644 libs/kfs/quickmount.c
> create mode 100644 libs/kfs/ramfile.c
> create mode 100644 libs/kfs/readheadfile.c
> create mode 100644 libs/kfs/report.c
> create mode 100644 libs/kfs/unix/syslockfile.c
> delete mode 100644 libs/kfs/unix/syspath.c
> create mode 100644 libs/kfs/win/syslockfile.c
> delete mode 100644 libs/kfs/win/syspath.c
> create mode 100644 libs/klib/Judy.h
> mode change 100755 => 100644 libs/klib/SHA-32bit.c
> mode change 100755 => 100644 libs/klib/SHA-64bit.c
> create mode 100644 libs/klib/judy-vector.c
> create mode 100644 libs/klib/judy/Judy1.h
> create mode 100644 libs/klib/judy/JudyByCount.c
> create mode 100644 libs/klib/judy/JudyByCountWithDefs.c
> create mode 100644 libs/klib/judy/JudyCascade.c
> create mode 100644 libs/klib/judy/JudyCount.c
> create mode 100644 libs/klib/judy/JudyCreateBranch.c
> create mode 100644 libs/klib/judy/JudyDecascade.c
> create mode 100644 libs/klib/judy/JudyDel.c
> create mode 100644 libs/klib/judy/JudyFirst.c
> create mode 100644 libs/klib/judy/JudyFreeArray.c
> create mode 100644 libs/klib/judy/JudyGet.c
> create mode 100644 libs/klib/judy/JudyHS.c
> create mode 100644 libs/klib/judy/JudyHS.h
> create mode 100644 libs/klib/judy/JudyIns.c
> create mode 100644 libs/klib/judy/JudyInsArray.c
> create mode 100644 libs/klib/judy/JudyInsertBranch.c
> create mode 100644 libs/klib/judy/JudyL.h
> create mode 100644 libs/klib/judy/JudyMalloc.c
> create mode 100644 libs/klib/judy/JudyMallocIF.c
> create mode 100644 libs/klib/judy/JudyMemActive.c
> create mode 100644 libs/klib/judy/JudyMemUsed.c
> create mode 100644 libs/klib/judy/JudyNext.c
> create mode 100644 libs/klib/judy/JudyNextEmpty.c
> create mode 100644 libs/klib/judy/JudyPrev.c
> create mode 100644 libs/klib/judy/JudyPrevEmpty.c
> create mode 100644 libs/klib/judy/JudyPrevNext.c
> create mode 100644 libs/klib/judy/JudyPrevNextEmpty.c
> 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
> create mode 100644 libs/klib/judy/j__udyGet.c
> create mode 100644 libs/klib/ksort.c
> delete mode 100644 libs/klib/libklib.vers.h
> create mode 100644 libs/klib/report.c
> mode change 100755 => 100644 libs/klib/win/systime.c
> 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
> create mode 100644 libs/kns/kns_mgr_priv.h
> copy libs/{align/libalign-writer.vers => kns/libkns.vers} (100%)
> 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
> create mode 100644 libs/krypto/aes-ncbi.vecreg.pic.o.list
> 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
> create mode 100644 libs/krypto/blockcipher-priv.h
> create mode 100644 libs/krypto/blockcipher.c
> create mode 100644 libs/krypto/cipher-byte.c
> create mode 100644 libs/krypto/cipher-impl.h
> create mode 100644 libs/krypto/cipher-no-vec.c
> create mode 100644 libs/krypto/cipher-priv.h
> create mode 100644 libs/krypto/cipher-vec.aes-ni.pic.o.list
> create mode 100644 libs/krypto/cipher-vec.c
> create mode 100644 libs/krypto/cipher-vec.vec.pic.o.list
> create mode 100644 libs/krypto/cipher-vec.vecreg.pic.o.list
> create mode 100644 libs/krypto/cipher.c
> create mode 100644 libs/krypto/ciphermgr.c
> create mode 100644 libs/krypto/compile-test.aes-ni.pic.o.list
> create mode 100644 libs/krypto/compile-test.c
> create mode 100644 libs/krypto/compile-test.vec.pic.o.list
> create mode 100644 libs/krypto/compile-test.vecreg.pic.o.list
> create mode 100644 libs/krypto/csprng.c
> create mode 100644 libs/krypto/encfile-priv.h
> create mode 100644 libs/krypto/encfile.c
> create mode 100644 libs/krypto/encfilev2.c
> create mode 100644 libs/krypto/key.c
> create mode 100644 libs/krypto/libkrypto.vers
> copy libs/{align/libalign-writer.vers => krypto/libkryptotest.vers} (100%)
> create mode 100644 libs/krypto/manager.c
> create mode 100644 libs/krypto/ncbi-priv.h
> create mode 100644 libs/krypto/no-null-ncbi.aes-ni.pic.o.list
> create mode 100644 libs/krypto/no-null-ncbi.c
> create mode 100644 libs/krypto/no-null-ncbi.vec.pic.o.list
> create mode 100644 libs/krypto/no-null-ncbi.vecreg.pic.o.list
> create mode 100644 libs/krypto/null-ncbi-priv.h
> create mode 100644 libs/krypto/null-ncbi.c
> create mode 100644 libs/krypto/null-ncbi.vec.pic.o.list
> create mode 100644 libs/krypto/null-ncbi.vecreg.pic.o.list
> 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
> create mode 100644 libs/ktst/testenv.cpp
> create mode 100644 libs/ktst/testrunner.cpp
> create mode 100644 libs/ktst/unix/runprocesstestcase.cpp
> create mode 100644 libs/ktst/win/runprocesstestcase.cpp
> create mode 100644 libs/loader/Makefile
> create mode 100644 libs/loader/alignment-writer.c
> create mode 100644 libs/loader/common-reader.c
> create mode 100644 libs/loader/common-writer.c
> create mode 100644 libs/loader/mmarray.c
> create mode 100644 libs/loader/reference-writer.c
> create mode 100644 libs/loader/sequence-writer.c
> delete mode 100644 libs/search/libksrch.vers.h
> delete mode 100644 libs/sra/libsradb.vers.h
> delete mode 100644 libs/sra/libsrareader.vers.h
> delete mode 100644 libs/sra/libsraschema.vers.h
> delete mode 100644 libs/sra/libwsradb.vers.h
> delete mode 100644 libs/sra/libwsraschema.vers.h
> create mode 100644 libs/sra/sracache.c
> delete mode 100644 libs/sra/srapath-stub.c
> mode change 100755 => 100644 libs/sra/wsraschema-stub.c
> create mode 100644 libs/sraxf/fix_read_seg_impl.h
> delete mode 100644 libs/sraxf/libsraxf.vers.h
> delete mode 100644 libs/sraxf/libwsraxf.vers.h
> mode change 100755 => 100644 libs/sraxf/varloc.c
> create mode 100644 libs/vdb/database-depend.c
> create mode 100644 libs/vdb/delta_average.c
> delete mode 100644 libs/vdb/libvdb.vers.h
> delete mode 100644 libs/vdb/libwvdb.vers.h
> create mode 100644 libs/vdb/report-vdb.c
> create mode 100644 libs/vfs/Makefile
> create mode 100644 libs/vfs/libsrapath.vers
> create mode 100644 libs/vfs/libvfs.vers
> create mode 100644 libs/vfs/manager.c
> create mode 100644 libs/vfs/path-priv.h
> create mode 100644 libs/vfs/path.c
> create mode 100644 libs/vfs/resolver-priv.h
> create mode 100644 libs/vfs/resolver.c
> create mode 100644 libs/vfs/srapath-stub.c
> create mode 100644 libs/vfs/srapath.c
> create mode 100644 libs/vfs/unix/syspath.c
> create mode 100644 libs/vfs/win/syspath.c
> delete mode 100644 libs/vxf/libvxf.vers.h
> create mode 100644 libs/vxf/lower-case-tech-reads.c
> create mode 100644 libs/vxf/wgs-tokenize-accession.c
> create mode 100644 libs/wgsxf/Makefile
> create mode 100644 libs/wgsxf/build_read_type.c
> create mode 100644 libs/wgsxf/build_scaffold.c
> copy libs/{align/libalign-writer.vers => wgsxf/libwgsxf.vers} (100%)
> rename libs/{align/libalign-writer.vers => wgsxf/libwwgsxf.vers} (100%)
> delete mode 100644 tools/align-info/align-info.vers.h
> create mode 100644 tools/bam-loader/Globals.h
> create mode 100644 tools/bam-loader/KFileHelper.c
> create mode 100644 tools/bam-loader/KFileHelper.h
> create mode 100644 tools/bam-loader/KVPFile.c
> create mode 100644 tools/bam-loader/KVPFile.h
> create mode 100644 tools/bam-loader/Makefile
> create mode 100644 tools/bam-loader/alignment-writer.c
> create mode 100644 tools/bam-loader/alignment-writer.h
> create mode 100644 tools/bam-loader/analysis.c
> create mode 100644 tools/bam-loader/analysis.h
> create mode 100644 tools/bam-loader/bam-load.vers
> create mode 100644 tools/bam-loader/bam-loader.c
> create mode 100644 tools/bam-loader/hashtable.c
> create mode 100644 tools/bam-loader/hashtable.h
> create mode 100644 tools/bam-loader/loader-imp.c
> create mode 100644 tools/bam-loader/loader-imp.h
> create mode 100644 tools/bam-loader/reference-writer.c
> create mode 100644 tools/bam-loader/reference-writer.h
> create mode 100644 tools/bam-loader/sequence-writer.c
> create mode 100644 tools/bam-loader/sequence-writer.h
> create mode 100644 tools/cg-load/Makefile
> create mode 100644 tools/cg-load/cg-load.c
> create mode 100644 tools/cg-load/cg-load.vers
> create mode 100644 tools/cg-load/debug.h
> create mode 100644 tools/cg-load/defs.h
> create mode 100644 tools/cg-load/f1_3.c
> create mode 100644 tools/cg-load/f1_5.c
> create mode 100644 tools/cg-load/f2_0.c
> create mode 100644 tools/cg-load/f2_2.c
> create mode 100644 tools/cg-load/factory-cmn.h
> create mode 100644 tools/cg-load/factory-evidence-dnbs.c
> create mode 100644 tools/cg-load/factory-evidence-dnbs.h
> create mode 100644 tools/cg-load/factory-evidence-intervals.c
> create mode 100644 tools/cg-load/factory-evidence-intervals.h
> create mode 100644 tools/cg-load/factory-file.h
> create mode 100644 tools/cg-load/factory-mappings.c
> create mode 100644 tools/cg-load/factory-mappings.h
> create mode 100644 tools/cg-load/factory-reads.c
> create mode 100644 tools/cg-load/factory-reads.h
> create mode 100644 tools/cg-load/file-version-factory.c
> create mode 100644 tools/cg-load/file.c
> create mode 100644 tools/cg-load/file.h
> create mode 100644 tools/cg-load/writer-algn.c
> create mode 100644 tools/cg-load/writer-algn.h
> create mode 100644 tools/cg-load/writer-evidence-dnbs.c
> create mode 100644 tools/cg-load/writer-evidence-dnbs.h
> create mode 100644 tools/cg-load/writer-evidence-intervals.c
> create mode 100644 tools/cg-load/writer-evidence-intervals.h
> create mode 100644 tools/cg-load/writer-seq.c
> create mode 100644 tools/cg-load/writer-seq.h
> create mode 100644 tools/fastq-loader/Makefile
> create mode 100644 tools/fastq-loader/fastq-grammar.c
> create mode 100644 tools/fastq-loader/fastq-grammar.y
> create mode 100644 tools/fastq-loader/fastq-lex.c
> create mode 100644 tools/fastq-loader/fastq-lex.l
> create mode 100644 tools/fastq-loader/fastq-loader.c
> create mode 100644 tools/fastq-loader/fastq-parse.h
> create mode 100644 tools/fastq-loader/fastq-reader.c
> create mode 100644 tools/fastq-loader/fastq-reader.h
> create mode 100644 tools/fastq-loader/fastq-tokens.h
> create mode 100644 tools/fastq-loader/latf-load.vers
> create mode 100644 tools/fastq-loader/loader-imp.c
> delete mode 100644 tools/kar/kar.vers.h
> delete mode 100644 tools/kar/sra-kar.vers.h
> create mode 100644 tools/nenctool/Makefile
> create mode 100644 tools/nenctool/nenctest.c
> create mode 100644 tools/nenctool/nenctest.vers
> create mode 100644 tools/nenctool/nenctool.c
> create mode 100644 tools/nenctool/nenctool.vers
> create mode 100644 tools/nencvalid/Makefile
> create mode 100644 tools/nencvalid/nencvalid.c
> create mode 100644 tools/nencvalid/nencvalid.vers
> create mode 100644 tools/prefetch/Makefile
> create mode 100644 tools/prefetch/prefetch.c
> create mode 100644 tools/prefetch/prefetch.vers
> mode change 100755 => 100644 tools/refseq-load/Makefile
> delete mode 100644 tools/refseq-load/refseq-load.vers.h
> delete mode 100644 tools/sam-dump/sam-dump.vers.h
> delete mode 100644 tools/sra-dbcc/sra-dbcc.vers.h
> delete mode 100644 tools/sra-dump/abi-dump.vers.h
> create mode 100644 tools/sra-dump/fasta_dump.c
> create mode 100644 tools/sra-dump/fasta_dump.h
> delete mode 100644 tools/sra-dump/fastq-dump.vers.h
> delete mode 100644 tools/sra-dump/illumina-dump.vers.h
> delete mode 100644 tools/sra-dump/sff-dump.vers.h
> delete mode 100644 tools/sra-dump/sra-dump.vers.h
> delete mode 100644 tools/sra-load/abi-load.vers.h
> delete mode 100644 tools/sra-load/fastq-load.vers.h
> delete mode 100644 tools/sra-load/helicos-load.vers.h
> delete mode 100644 tools/sra-load/illumina-load.vers.h
> delete mode 100644 tools/sra-load/sff-load.vers.h
> delete mode 100644 tools/sra-load/srf-load.vers.h
> create mode 100644 tools/sra-pileup/Makefile
> create mode 100644 tools/sra-pileup/cg_tools.c
> create mode 100644 tools/sra-pileup/cg_tools.h
> create mode 100644 tools/sra-pileup/cmdline_cmn.c
> create mode 100644 tools/sra-pileup/cmdline_cmn.h
> copy tools/{sam-dump => sra-pileup}/debug.h (100%)
> create mode 100644 tools/sra-pileup/inputfiles.c
> create mode 100644 tools/sra-pileup/inputfiles.h
> create mode 100644 tools/sra-pileup/matecache.c
> create mode 100644 tools/sra-pileup/matecache.h
> create mode 100644 tools/sra-pileup/out_redir.c
> create mode 100644 tools/sra-pileup/out_redir.h
> create mode 100644 tools/sra-pileup/read_fkt.c
> create mode 100644 tools/sra-pileup/read_fkt.h
> create mode 100644 tools/sra-pileup/reref.c
> create mode 100644 tools/sra-pileup/reref.h
> create mode 100644 tools/sra-pileup/sam-aligned.c
> create mode 100644 tools/sra-pileup/sam-aligned.h
> create mode 100644 tools/sra-pileup/sam-dump-opts.c
> create mode 100644 tools/sra-pileup/sam-dump-opts.h
> create mode 100644 tools/sra-pileup/sam-dump.c
> create mode 100644 tools/sra-pileup/sam-dump.vers
> create mode 100644 tools/sra-pileup/sam-dump3.c
> create mode 100644 tools/sra-pileup/sam-hdr.c
> create mode 100644 tools/sra-pileup/sam-hdr.h
> create mode 100644 tools/sra-pileup/sam-unaligned.c
> create mode 100644 tools/sra-pileup/sam-unaligned.h
> create mode 100644 tools/sra-pileup/sra-pileup.c
> create mode 100644 tools/sra-pileup/sra-pileup.vers
> create mode 100644 tools/sra-sort/Makefile
> create mode 100644 tools/sra-sort/Makefile.cc
> create mode 100644 tools/sra-sort/Makefile.clang
> create mode 100644 tools/sra-sort/Makefile.gcc
> create mode 100644 tools/sra-sort/Makefile.vc++
> create mode 100644 tools/sra-sort/buff-writer.c
> create mode 100644 tools/sra-sort/buff-writer.h
> create mode 100644 tools/sra-sort/caps.c
> create mode 100644 tools/sra-sort/caps.h
> create mode 100644 tools/sra-sort/capture-first-half-aligned.c
> create mode 100644 tools/sra-sort/col-pair.c
> create mode 100644 tools/sra-sort/col-pair.h
> create mode 100644 tools/sra-sort/csra-pair.c
> create mode 100644 tools/sra-sort/csra-pair.h
> create mode 100644 tools/sra-sort/csra-tbl.c
> create mode 100644 tools/sra-sort/csra-tbl.h
> create mode 100644 tools/sra-sort/ctx.h
> create mode 100644 tools/sra-sort/db-pair.c
> create mode 100644 tools/sra-sort/db-pair.h
> create mode 100644 tools/sra-sort/dir-pair.c
> create mode 100644 tools/sra-sort/dir-pair.h
> create mode 100644 tools/sra-sort/dump-blob-boundaries.c
> create mode 100644 tools/sra-sort/except.c
> create mode 100644 tools/sra-sort/except.h
> create mode 100755 tools/sra-sort/gcc-ped.sh
> create mode 100644 tools/sra-sort/glob-poslen.c
> create mode 100644 tools/sra-sort/glob-poslen.h
> create mode 100644 tools/sra-sort/id-mapper-col.c
> create mode 100644 tools/sra-sort/id-mapper-col.h
> create mode 100644 tools/sra-sort/idx-mapping.c
> create mode 100644 tools/sra-sort/idx-mapping.h
> create mode 100644 tools/sra-sort/map-file.c
> create mode 100644 tools/sra-sort/map-file.h
> create mode 100644 tools/sra-sort/mapping-row-set.c
> create mode 100644 tools/sra-sort/mem.c
> create mode 100644 tools/sra-sort/mem.h
> create mode 100644 tools/sra-sort/membank-priv.h
> create mode 100644 tools/sra-sort/membank.c
> create mode 100644 tools/sra-sort/meta-pair.c
> create mode 100644 tools/sra-sort/meta-pair.h
> create mode 100644 tools/sra-sort/paged-membank.c
> create mode 100644 tools/sra-sort/paged-mmapbank.c
> create mode 100644 tools/sra-sort/poslen-col-pair.c
> create mode 100644 tools/sra-sort/poslen-col-pair.h
> create mode 100644 tools/sra-sort/ref-alignid-col.c
> create mode 100644 tools/sra-sort/ref-alignid-col.h
> create mode 100644 tools/sra-sort/row-set-priv.h
> create mode 100644 tools/sra-sort/row-set.c
> create mode 100644 tools/sra-sort/row-set.h
> create mode 100644 tools/sra-sort/run.c
> create mode 100644 tools/sra-sort/simple-row-set.c
> create mode 100644 tools/sra-sort/sort-defs.h
> create mode 100644 tools/sra-sort/sorting-row-set.c
> create mode 100644 tools/sra-sort/sra-sort.c
> create mode 100644 tools/sra-sort/sra-sort.h
> create mode 100644 tools/sra-sort/sra-sort.vers
> create mode 100644 tools/sra-sort/status.h
> create mode 100644 tools/sra-sort/tbl-pair.c
> create mode 100644 tools/sra-sort/tbl-pair.h
> create mode 100644 tools/sra-sort/xcheck-ref-align.c
> create mode 100644 tools/sra-sort/xcheck.h
> delete mode 100644 tools/sra-stat/sra-stat.vers.h
> create mode 100644 tools/srapath/Makefile
> create mode 100644 tools/srapath/srapath.c
> create mode 100644 tools/srapath/srapath.vers
> delete mode 100644 tools/util/kdbmeta.vers.h
> create mode 100644 tools/util/mac/syspass.c
> delete mode 100644 tools/util/rcexplain.vers.h
> create mode 100644 tools/util/syspass-priv.h
> create mode 100644 tools/util/test-sra.c
> create mode 100644 tools/util/test-sra.vers
> create mode 100644 tools/util/unix/syspass.c
> delete mode 100644 tools/util/vdb-lock.vers.h
> create mode 100644 tools/util/vdb-passwd.c
> create mode 100644 tools/util/vdb-passwd.vers
> delete mode 100644 tools/util/vdb-unlock.vers.h
> create mode 100644 tools/util/win/syspass.c
> delete mode 100644 tools/vdb-config/vdb-config.vers.h
> delete mode 100644 tools/vdb-copy/vdb-copy.vers.h
> create mode 100644 tools/vdb-decrypt/Makefile
> create mode 100644 tools/vdb-decrypt/shared.c
> create mode 100644 tools/vdb-decrypt/shared.h
> create mode 100644 tools/vdb-decrypt/vdb-decrypt.c
> create mode 100644 tools/vdb-decrypt/vdb-decrypt.vers
> create mode 100644 tools/vdb-decrypt/vdb-encrypt.c
> create mode 100644 tools/vdb-decrypt/vdb-encrypt.vers
> delete mode 100644 tools/vdb-dump/vdb-dump.vers.h
> create mode 100644 tools/vdb-validate/Makefile
> create mode 100644 tools/vdb-validate/vdb-validate.c
> create mode 100644 tools/vdb-validate/vdb-validate.vers
>
> --
> Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git
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