[med-svn] [sra-sdk] branch upstream updated (ba954f7 -> 46a4f38)
Andreas Tille
tille at debian.org
Tue Aug 13 13:34:26 UTC 2013
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 +-
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
More information about the debian-med-commit
mailing list