[med-svn] [sra-sdk] 05/06: Merge tag 'upstream/2.7.0'
Andreas Tille
tille at debian.org
Thu Jul 21 15:51:52 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 7b31da5147024bca65d288b80f0cfd6cdce5d38f
Merge: 0ad04b9 c81075b
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 21 16:27:11 2016 +0200
Merge tag 'upstream/2.7.0'
Upstream version 2.7.0
.gitignore | 31 +-
CHANGES | 83 +-
CHANGES.md | 80 +-
LICENSE | 13 +-
Makefile | 41 +-
README | 18 +-
README-blastn | 133 -
README-vdb-config | 115 -
README.md | 16 +-
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interfaces/align/reference.h | 150 +
interfaces/align/refseq-mgr.h | 88 +
interfaces/align/refseq.vschema | 100 +
interfaces/align/seq.vschema | 300 +
interfaces/align/writer-alignment.h | 181 +
interfaces/align/writer-cmn.h | 46 +
interfaces/align/writer-reference.h | 180 +
interfaces/align/writer-refseq.h | 89 +
interfaces/align/writer-sequence.h | 157 +
interfaces/cc/cc/compiler.h | 39 +
interfaces/cc/gcc/compiler.h | 39 +
interfaces/cc/gcc/fat86/arch-impl.h | 33 +
interfaces/cc/gcc/fat86/atomic.h | 33 +
interfaces/cc/gcc/fat86/atomic32.h | 37 +
interfaces/cc/gcc/fat86/atomic64.h | 32 +
interfaces/cc/gcc/fat86/bitstr.h | 33 +
interfaces/cc/gcc/fat86/byteswap.h | 33 +
interfaces/cc/gcc/fat86/strtol.h | 33 +
interfaces/cc/gcc/i386/arch-impl.h | 488 +
interfaces/cc/gcc/i386/atomic.h | 169 +
interfaces/cc/gcc/i386/atomic32.h | 366 +
interfaces/cc/gcc/i386/bitstr.h | 39 +
interfaces/cc/gcc/i386/byteswap.h | 89 +
interfaces/cc/gcc/i386/strtol.h | 67 +
interfaces/cc/gcc/noarch/bitstr.h | 413 +
interfaces/cc/gcc/ppc32/arch-impl.h | 209 +
interfaces/cc/gcc/ppc32/atomic.h | 157 +
interfaces/cc/gcc/ppc32/atomic32.h | 197 +
interfaces/cc/gcc/ppc32/bitstr.h | 40 +
interfaces/cc/gcc/ppc32/strtol.h | 67 +
interfaces/cc/gcc/v128.h | 1093 +
interfaces/cc/gcc/va_copy.h | 49 +
interfaces/cc/gcc/x86_64/arch-impl.h | 459 +
interfaces/cc/gcc/x86_64/atomic.h | 183 +
interfaces/cc/gcc/x86_64/atomic32.h | 365 +
interfaces/cc/gcc/x86_64/atomic64.h | 365 +
interfaces/cc/gcc/x86_64/bitstr.h | 39 +
interfaces/cc/gcc/x86_64/byteswap.h | 89 +
interfaces/cc/gcc/x86_64/strtol.h | 69 +
interfaces/cc/icc/compiler.h | 39 +
interfaces/cc/vc++/compiler.h | 72 +
interfaces/cc/vc++/i386/arch-impl.h | 42 +
interfaces/cc/vc++/i386/bitstr.h | 39 +
interfaces/cc/vc++/noarch/arch-impl.h | 378 +
interfaces/cc/vc++/noarch/bitstr.h | 412 +
interfaces/cc/vc++/stdbool.h | 46 +
interfaces/cc/vc++/stdint.h | 50 +
interfaces/cc/vc++/va_copy.h | 43 +
interfaces/cc/vc++/x86_64/arch-impl.h | 42 +
interfaces/cc/vc++/x86_64/bitstr.h | 39 +
interfaces/csra2/csra2.vschema | 42 +
interfaces/csra2/read.vschema | 255 +
interfaces/csra2/reference.vschema | 245 +
interfaces/csra2/stats.vschema | 92 +
interfaces/ext/bzlib.h | 282 +
interfaces/ext/hdf5/H5ACpublic.h | 508 +
interfaces/ext/hdf5/H5AbstractDs.h | 91 +
interfaces/ext/hdf5/H5Apublic.h | 120 +
interfaces/ext/hdf5/H5ArrayType.h | 62 +
interfaces/ext/hdf5/H5AtomType.h | 81 +
interfaces/ext/hdf5/H5Attribute.h | 98 +
interfaces/ext/hdf5/H5Classes.h | 51 +
interfaces/ext/hdf5/H5CommonFG.h | 172 +
interfaces/ext/hdf5/H5CompType.h | 114 +
interfaces/ext/hdf5/H5Cpp.h | 58 +
interfaces/ext/hdf5/H5CppDoc.h | 91 +
interfaces/ext/hdf5/H5Cpublic.h | 61 +
interfaces/ext/hdf5/H5DSpublic.h | 79 +
interfaces/ext/hdf5/H5DataSet.h | 132 +
interfaces/ext/hdf5/H5DataSpace.h | 131 +
interfaces/ext/hdf5/H5DataType.h | 139 +
interfaces/ext/hdf5/H5DcreatProp.h | 126 +
interfaces/ext/hdf5/H5Dpublic.h | 154 +
interfaces/ext/hdf5/H5DxferProp.h | 111 +
interfaces/ext/hdf5/H5EnumType.h | 77 +
interfaces/ext/hdf5/H5Epubgen.h | 360 +
interfaces/ext/hdf5/H5Epublic.h | 228 +
interfaces/ext/hdf5/H5Exception.h | 164 +
interfaces/ext/hdf5/H5FDcore.h | 42 +
interfaces/ext/hdf5/H5FDdirect.h | 57 +
interfaces/ext/hdf5/H5FDfamily.h | 44 +
interfaces/ext/hdf5/H5FDlog.h | 69 +
interfaces/ext/hdf5/H5FDmpi.h | 123 +
interfaces/ext/hdf5/H5FDmpio.h | 65 +
interfaces/ext/hdf5/H5FDmpiposix.h | 56 +
interfaces/ext/hdf5/H5FDmulti.h | 52 +
interfaces/ext/hdf5/H5FDpublic.h | 279 +
interfaces/ext/hdf5/H5FDsec2.h | 42 +
interfaces/ext/hdf5/H5FDstdio.h | 41 +
interfaces/ext/hdf5/H5FaccProp.h | 142 +
interfaces/ext/hdf5/H5FcreatProp.h | 79 +
interfaces/ext/hdf5/H5File.h | 148 +
interfaces/ext/hdf5/H5FloatType.h | 74 +
interfaces/ext/hdf5/H5Fpublic.h | 181 +
interfaces/ext/hdf5/H5Gpublic.h | 178 +
interfaces/ext/hdf5/H5Group.h | 76 +
interfaces/ext/hdf5/H5IMpublic.h | 87 +
interfaces/ext/hdf5/H5IdComponent.h | 99 +
interfaces/ext/hdf5/H5Include.h | 30 +
interfaces/ext/hdf5/H5IntType.h | 56 +
interfaces/ext/hdf5/H5Ipublic.h | 104 +
interfaces/ext/hdf5/H5LTpublic.h | 351 +
interfaces/ext/hdf5/H5Library.h | 70 +
interfaces/ext/hdf5/H5Lpublic.h | 202 +
interfaces/ext/hdf5/H5MMpublic.h | 47 +
interfaces/ext/hdf5/H5Object.h | 133 +
interfaces/ext/hdf5/H5Opublic.h | 203 +
interfaces/ext/hdf5/H5PTpublic.h | 127 +
interfaces/ext/hdf5/H5PacketTable.h | 244 +
interfaces/ext/hdf5/H5Ppublic.h | 432 +
interfaces/ext/hdf5/H5PredType.h | 250 +
interfaces/ext/hdf5/H5PropList.h | 122 +
interfaces/ext/hdf5/H5Rpublic.h | 92 +
interfaces/ext/hdf5/H5Spublic.h | 152 +
interfaces/ext/hdf5/H5StrType.h | 68 +
interfaces/ext/hdf5/H5TBpublic.h | 233 +
interfaces/ext/hdf5/H5Tpublic.h | 621 +
interfaces/ext/hdf5/H5VarLenType.h | 52 +
interfaces/ext/hdf5/H5Zpublic.h | 249 +
interfaces/ext/hdf5/H5api_adpt.h | 408 +
interfaces/ext/hdf5/H5f90i.h | 43 +
interfaces/ext/hdf5/H5f90i_gen.h | 48 +
interfaces/ext/hdf5/H5overflow.h | 1939 ++
interfaces/ext/hdf5/H5pubconf.h | 723 +
interfaces/ext/hdf5/H5public.h | 310 +
interfaces/ext/hdf5/H5version.h | 419 +
interfaces/ext/hdf5/h5_dble_interface.mod | 2194 ++
interfaces/ext/hdf5/h5a.mod | 2637 +++
interfaces/ext/hdf5/h5d.mod | 3040 +++
interfaces/ext/hdf5/h5e.mod | 1399 ++
interfaces/ext/hdf5/h5f.mod | 1513 ++
interfaces/ext/hdf5/h5fortran_types.mod | 73 +
interfaces/ext/hdf5/h5g.mod | 1600 ++
interfaces/ext/hdf5/h5global.mod | 1354 ++
interfaces/ext/hdf5/h5i.mod | 1421 ++
interfaces/ext/hdf5/h5im.mod | 16518 +++++++++++++++
interfaces/ext/hdf5/h5l.mod | 1568 ++
interfaces/ext/hdf5/h5lib.mod | 56 +
interfaces/ext/hdf5/h5lt.mod | 17284 ++++++++++++++++
interfaces/ext/hdf5/h5o.mod | 1398 ++
interfaces/ext/hdf5/h5p.mod | 2804 +++
interfaces/ext/hdf5/h5r.mod | 1458 ++
interfaces/ext/hdf5/h5s.mod | 1658 ++
interfaces/ext/hdf5/h5t.mod | 1943 ++
interfaces/ext/hdf5/h5tb.mod | 16846 ++++++++++++++++
interfaces/ext/hdf5/h5z.mod | 1383 ++
interfaces/ext/hdf5/hdf5.h | 55 +
interfaces/ext/hdf5/hdf5.mod | 16361 +++++++++++++++
interfaces/ext/hdf5/hdf5_hl.h | 32 +
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/ext/magic.h | 89 +
interfaces/ext/regex.h | 557 +
interfaces/ext/ricehdf.h | 86 +
interfaces/ext/zconf.h | 304 +
interfaces/ext/zlib.h | 1613 ++
interfaces/fastq/extern.h | 41 +
interfaces/fastq/fq-dump.h | 110 +
interfaces/hdf5/extern.h | 41 +
interfaces/hdf5/kdf5.h | 89 +
interfaces/insdc/insdc.h | 277 +
interfaces/insdc/insdc.vschema | 232 +
interfaces/insdc/seq.vschema | 210 +
interfaces/insdc/sra.h | 111 +
interfaces/insdc/sra.vschema | 467 +
interfaces/kapp/args-conv.h | 57 +
interfaces/kapp/args.h | 402 +
interfaces/kapp/extern.h | 47 +
interfaces/kapp/loader-file.h | 122 +
interfaces/kapp/loader-meta.h | 55 +
interfaces/kapp/log-xml.h | 76 +
interfaces/kapp/main.h | 174 +
interfaces/kapp/progressbar.h | 82 +
interfaces/kapp/queue-file.h | 149 +
interfaces/kdb/btree.h | 188 +
interfaces/kdb/column.h | 360 +
interfaces/kdb/consistency-check.h | 142 +
interfaces/kdb/database.h | 278 +
interfaces/kdb/extern.h | 41 +
interfaces/kdb/index.h | 309 +
interfaces/kdb/kdb-priv.h | 165 +
interfaces/kdb/manager.h | 182 +
interfaces/kdb/meta.h | 411 +
interfaces/kdb/meta.hpp | 487 +
interfaces/kdb/namelist.h | 81 +
interfaces/kdb/table.h | 298 +
interfaces/kfc/callconv.h | 53 +
interfaces/kfc/ctx.h | 198 +
interfaces/kfc/defs.h | 185 +
interfaces/kfc/except.h | 215 +
interfaces/kfc/extern.h | 68 +
interfaces/kfc/rc.h | 352 +
interfaces/kfc/refcount-impl.h | 95 +
interfaces/kfc/refcount.h | 246 +
interfaces/kfc/rsrc-global.h | 72 +
interfaces/kfc/rsrc.h | 89 +
interfaces/kfc/tstate.h | 107 +
interfaces/kfc/vtbl-impl.h | 139 +
interfaces/kfc/xc.h | 186 +
interfaces/kfc/xcdefs.h | 81 +
interfaces/kfc/xcext.h | 64 +
interfaces/kfc/xcgen.h | 68 +
interfaces/kfg/config.h | 425 +
interfaces/kfg/extern.h | 41 +
interfaces/kfg/kart.h | 90 +
interfaces/kfg/keystore-priv.h | 92 +
interfaces/kfg/keystore.h | 159 +
interfaces/kfg/kfg-priv.h | 98 +
interfaces/kfg/ngc.h | 67 +
interfaces/kfg/properties.h | 137 +
interfaces/kfg/repository.h | 421 +
interfaces/kfs/arc.h | 143 +
interfaces/kfs/arrayfile.h | 180 +
interfaces/kfs/buffile.h | 94 +
interfaces/kfs/bzip.h | 77 +
interfaces/kfs/cacheteefile.h | 162 +
interfaces/kfs/countfile.h | 73 +
interfaces/kfs/crc.h | 292 +
interfaces/kfs/defs.h | 121 +
interfaces/kfs/directory.h | 591 +
interfaces/kfs/directory.hpp | 582 +
interfaces/kfs/dyload.h | 223 +
interfaces/kfs/extendable-ramfile.h | 50 +
interfaces/kfs/extern.h | 41 +
interfaces/kfs/ffext.h | 48 +
interfaces/kfs/ffmagic.h | 49 +
interfaces/kfs/file-impl.h | 193 +
interfaces/kfs/file-v1.h | 259 +
interfaces/kfs/file-v2.h | 264 +
interfaces/kfs/file.h | 99 +
interfaces/kfs/file.hpp | 147 +
interfaces/kfs/fileformat.h | 140 +
interfaces/kfs/filetools.h | 86 +
interfaces/kfs/gzip.h | 77 +
interfaces/kfs/impl.h | 319 +
interfaces/kfs/kfs-priv.h | 99 +
interfaces/kfs/lockfile.h | 116 +
interfaces/kfs/manager.h | 31 +
interfaces/kfs/md5.h | 289 +
interfaces/kfs/mmap.h | 134 +
interfaces/kfs/nullfile.h | 62 +
interfaces/kfs/pagefile.h | 191 +
interfaces/kfs/path-priv.h | 32 +
interfaces/kfs/path.h | 32 +
interfaces/kfs/pmem.h | 156 +
interfaces/kfs/quickmount.h | 61 +
interfaces/kfs/ramfile.h | 75 +
interfaces/kfs/readheadfile.h | 86 +
interfaces/kfs/sra.h | 191 +
interfaces/kfs/subfile.h | 64 +
interfaces/kfs/szip.h | 77 +
interfaces/kfs/tar.h | 94 +
interfaces/kfs/teefile.h | 66 +
interfaces/kfs/toc.h | 148 +
interfaces/kfs/wgaencrypt.h | 27 +
interfaces/klib/btree.h | 147 +
interfaces/klib/callconv.h | 34 +
interfaces/klib/checksum.h | 152 +
interfaces/klib/container.h | 455 +
interfaces/klib/data-buffer.h | 206 +
interfaces/klib/debug.h | 549 +
interfaces/klib/defs.h | 147 +
interfaces/klib/extern.h | 51 +
interfaces/klib/impl.h | 96 +
interfaces/klib/klib-priv.h | 108 +
interfaces/klib/ksort-macro.h | 257 +
interfaces/klib/log.h | 381 +
interfaces/klib/logfmt.h | 62 +
interfaces/klib/misc.h | 51 +
interfaces/klib/namelist.h | 227 +
interfaces/klib/namelist.hpp | 130 +
interfaces/klib/ncbi-vdb-version.h | 56 +
interfaces/klib/num-gen.h | 228 +
interfaces/klib/out.h | 86 +
interfaces/klib/pack.h | 138 +
interfaces/klib/path-priv.h | 266 +
interfaces/klib/path.h | 252 +
interfaces/klib/pbstree.h | 287 +
interfaces/klib/printf.h | 406 +
interfaces/klib/progressbar.h | 85 +
interfaces/klib/ptrie.h | 296 +
interfaces/klib/rc.h | 185 +
interfaces/klib/refcount.h | 102 +
interfaces/klib/report.h | 103 +
interfaces/klib/sort.h | 123 +
interfaces/klib/sra-release-version.h | 99 +
interfaces/klib/status.h | 147 +
interfaces/klib/symbol.h | 146 +
interfaces/klib/symtab.h | 225 +
interfaces/klib/text.h | 557 +
interfaces/klib/time.h | 100 +
interfaces/klib/token.h | 254 +
interfaces/klib/trie.h | 293 +
interfaces/klib/vector.h | 539 +
interfaces/klib/vlen-encode.h | 161 +
interfaces/klib/writer.h | 170 +
interfaces/kns/adapt.h | 89 +
interfaces/kns/ascp.h | 101 +
interfaces/kns/endpoint.h | 147 +
interfaces/kns/extern.h | 41 +
interfaces/kns/http.h | 376 +
interfaces/kns/impl.h | 111 +
interfaces/kns/kns-mgr-priv.h | 103 +
interfaces/kns/manager-ext.h | 59 +
interfaces/kns/manager.h | 103 +
interfaces/kns/socket.h | 144 +
interfaces/kns/stream.h | 222 +
interfaces/kproc/barrier.h | 75 +
interfaces/kproc/barrier.hpp | 79 +
interfaces/kproc/cond.h | 103 +
interfaces/kproc/cond.hpp | 107 +
interfaces/kproc/extern.h | 41 +
interfaces/kproc/impl.h | 104 +
interfaces/kproc/lock.h | 144 +
interfaces/kproc/lock.hpp | 163 +
interfaces/kproc/procmgr.h | 120 +
interfaces/kproc/q-extern.h | 41 +
interfaces/kproc/queue.h | 116 +
interfaces/kproc/sem.h | 138 +
interfaces/kproc/sem.hpp | 134 +
interfaces/kproc/task.h | 83 +
interfaces/kproc/thread.h | 91 +
interfaces/kproc/thread.hpp | 98 +
interfaces/kproc/timeout.h | 68 +
interfaces/krypto/aes-priv.h | 1 +
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 | 48 +
interfaces/krypto/key.h | 103 +
interfaces/krypto/manager-priv.h | 26 +
interfaces/krypto/manager.h | 33 +
interfaces/krypto/reencfile.h | 94 +
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 | 22 +
interfaces/ktst/unit_test.hpp | 260 +
interfaces/ktst/unit_test_suite.hpp | 513 +
interfaces/kxml/xml.h | 382 +
interfaces/kxml/xml.hpp | 198 +
interfaces/loader/alignment-writer.h | 108 +
interfaces/loader/common-reader-priv.h | 300 +
interfaces/loader/common-reader.h | 486 +
interfaces/loader/common-writer.h | 192 +
interfaces/loader/mmarray.h | 50 +
interfaces/loader/reference-writer.h | 80 +
interfaces/loader/sequence-writer.h | 93 +
interfaces/ncbi/clip.vschema | 147 +
interfaces/ncbi/extern.h | 41 +
interfaces/ncbi/kimpl-sra-cgi.h | 91 +
interfaces/ncbi/ksra-cgi-lib.h | 52 +
interfaces/ncbi/ksra-cgi.h | 111 +
interfaces/ncbi/ncbi.h | 73 +
interfaces/ncbi/ncbi.vschema | 195 +
interfaces/ncbi/pnbrdb.vschema | 98 +
interfaces/ncbi/seq-graph.vschema | 180 +
interfaces/ncbi/seq.vschema | 894 +
interfaces/ncbi/spotname.h | 150 +
interfaces/ncbi/spotname.vschema | 377 +
interfaces/ncbi/sra.vschema | 758 +
interfaces/ncbi/stats.vschema | 119 +
interfaces/ncbi/varloc.vschema | 204 +
interfaces/ncbi/vdb-blast-priv.h | 53 +
interfaces/ncbi/vdb-blast.h | 606 +
interfaces/ncbi/wgs-contig.h | 183 +
interfaces/ncbi/wgs-contig.vschema | 695 +
interfaces/ngs/Model.graphml | 801 +
interfaces/ngs/NOTES.txt | 9 +
interfaces/ngs/SimpleModel.graphml | 395 +
interfaces/ngs/cstdint | 1 +
interfaces/ngs/ncbi/NGS.hpp | 95 +
interfaces/os/linux/os-native.h | 43 +
interfaces/os/mac/byteswap.h | 39 +
interfaces/os/mac/endian.h | 39 +
interfaces/os/mac/os-native.h | 114 +
interfaces/os/sun/arch-impl.h | 287 +
interfaces/os/sun/atomic.h | 152 +
interfaces/os/sun/atomic32.h | 218 +
interfaces/os/sun/bitstr.h | 47 +
interfaces/os/sun/byteswap.h | 40 +
interfaces/os/sun/endian.h | 44 +
interfaces/os/sun/fmtdef.h | 42 +
interfaces/os/sun/noarch/bitstr.h | 417 +
interfaces/os/sun/os-native.h | 181 +
interfaces/os/sun/strtol.h | 67 +
interfaces/os/sun/va_copy.h | 49 +
interfaces/os/unix/oserror.h | 38 +
interfaces/os/unix/sysalloc.h | 40 +
interfaces/os/unix/unix-native.h | 58 +
interfaces/os/win/atomic.h | 149 +
interfaces/os/win/atomic32.h | 194 +
interfaces/os/win/atomic64.h | 194 +
interfaces/os/win/byteswap.h | 44 +
interfaces/os/win/endian.h | 42 +
interfaces/os/win/os-native.h | 238 +
interfaces/os/win/oserror.h | 41 +
interfaces/os/win/strtol.h | 158 +
interfaces/os/win/sysalloc.h | 69 +
interfaces/rdbms/rdbms.h | 362 +
interfaces/rdbms/sybase.h | 52 +
interfaces/search/extern.h | 41 +
interfaces/search/grep.h | 268 +
interfaces/search/nucstrstr.h | 153 +
interfaces/search/ref-variation.h | 159 +
interfaces/search/smith-waterman.h | 72 +
interfaces/simple/extern.h | 41 +
interfaces/simple/sra.hpp | 1127 ++
interfaces/sra/454.vschema | 289 +
interfaces/sra/abi.h | 167 +
interfaces/sra/abi.vschema | 241 +
interfaces/sra/extern.h | 41 +
interfaces/sra/fastq.h | 191 +
interfaces/sra/generic-fastq.vschema | 265 +
interfaces/sra/helicos.vschema | 85 +
interfaces/sra/illumina.h | 170 +
interfaces/sra/illumina.vschema | 408 +
interfaces/sra/impl.h | 121 +
interfaces/sra/ion-torrent.vschema | 117 +
interfaces/sra/nanopore.vschema | 84 +
interfaces/sra/pacbio.h | 66 +
interfaces/sra/pacbio.vschema | 307 +
interfaces/sra/path-extern.h | 41 +
interfaces/sra/pevents.vschema | 91 +
interfaces/sra/rd-extern.h | 41 +
interfaces/sra/sch-extern.h | 41 +
interfaces/sra/sff-file.h | 110 +
interfaces/sra/sff.h | 147 +
interfaces/sra/sradb-priv.h | 407 +
interfaces/sra/sradb.h | 545 +
interfaces/sra/sradb.hpp | 441 +
interfaces/sra/srapath.h | 181 +
interfaces/sra/srapath.hpp | 176 +
interfaces/sra/sraschema.h | 72 +
interfaces/sra/types.h | 350 +
interfaces/sra/wsradb.h | 242 +
interfaces/sra/wsradb.hpp | 591 +
interfaces/svdb/extern.h | 47 +
interfaces/svdb/svdb.h | 531 +
interfaces/tui/extern.h | 41 +
interfaces/tui/tui.h | 297 +
interfaces/tui/tui.hpp | 739 +
interfaces/tui/tui_dlg.h | 367 +
interfaces/vdb/blob.h | 154 +
interfaces/vdb/built-in.vschema | 412 +
interfaces/vdb/cursor.h | 490 +
interfaces/vdb/cursor.hpp | 388 +
interfaces/vdb/database.h | 334 +
interfaces/vdb/database.hpp | 347 +
interfaces/vdb/dependencies.h | 231 +
interfaces/vdb/extern.h | 47 +
interfaces/vdb/manager.h | 226 +
interfaces/vdb/manager.hpp | 386 +
interfaces/vdb/report.h | 92 +
interfaces/vdb/schema.h | 460 +
interfaces/vdb/schema.hpp | 252 +
interfaces/vdb/table.h | 424 +
interfaces/vdb/table.hpp | 328 +
interfaces/vdb/types.h | 39 +
interfaces/vdb/types.hpp | 230 +
interfaces/vdb/vdb-priv.h | 342 +
interfaces/vdb/vdb.h | 62 +
interfaces/vdb/vdb.vschema | 859 +
interfaces/vdb/xform.h | 826 +
interfaces/vfs/extern.h | 47 +
interfaces/vfs/keyring-priv.h | 52 +
interfaces/vfs/manager-priv.h | 152 +
interfaces/vfs/manager.h | 322 +
interfaces/vfs/path-priv.h | 266 +
interfaces/vfs/path.h | 294 +
interfaces/vfs/resolver.h | 263 +
interfaces/xfs/doc.h | 123 +
interfaces/xfs/editors.h | 310 +
interfaces/xfs/extern.h | 48 +
interfaces/xfs/handle.h | 106 +
interfaces/xfs/model.h | 248 +
interfaces/xfs/node.h | 217 +
interfaces/xfs/path.h | 227 +
interfaces/xfs/perm.h | 173 +
interfaces/xfs/tree.h | 176 +
interfaces/xfs/xfs-defs.h | 125 +
interfaces/xfs/xfs.h | 165 +
interfaces/xfs/xlog.h | 54 +
libs/Makefile | 89 +
libs/align/.gitignore | 1 +
libs/align/Makefile | 163 +
libs/align/al_iterator.c | 565 +
libs/align/align-access.c | 812 +
libs/align/align_mgr.c | 108 +
libs/align/bam-priv.h | 48 +
libs/align/bam.c | 5054 +++++
libs/align/debug.h | 77 +
libs/align/dna-reverse-cmpl.c | 80 +
libs/align/pl_iterator.c | 689 +
libs/align/quality-quantizer.c | 109 +
libs/align/reader-cmn.c | 317 +
libs/align/reader-cmn.h | 81 +
libs/align/reader-refseq.c | 279 +
libs/align/reader-wgs.c | 169 +
libs/align/reader-wgs.h | 58 +
libs/align/ref_iterator.c | 863 +
libs/align/reference-cmn.c | 43 +
libs/align/reference-cmn.h | 38 +
libs/align/reference.c | 1943 ++
libs/align/refseq-mgr-priv.h | 35 +
libs/align/refseq-mgr.c | 1273 ++
libs/align/writer-alignment.c | 440 +
libs/align/writer-cmn.c | 589 +
libs/align/writer-priv.h | 151 +
libs/align/writer-ref.c | 481 +
libs/align/writer-ref.h | 106 +
libs/align/writer-reference.c | 3186 +++
libs/align/writer-refseq.c | 179 +
libs/align/writer-sequence.c | 778 +
libs/ascp/Makefile | 87 +
libs/ascp/ascp-priv.h | 74 +
libs/ascp/ascp.c | 840 +
libs/ascp/linux/ascp-path.c | 119 +
libs/ascp/mac/ascp-path.c | 74 +
libs/ascp/unix/connect.c | 618 +
libs/ascp/win/ascp-path.c | 75 +
libs/ascp/win/connect.c | 525 +
libs/axf/.gitignore | 1 +
libs/axf/Makefile | 142 +
libs/axf/align-local_ref_id.c | 143 +
libs/axf/align-local_ref_start.c | 148 +
libs/axf/align-ref-name.c | 191 +
libs/axf/align-ref-pos.c | 299 +
libs/axf/align-ref-seq-id.c | 188 +
libs/axf/align-restore-read.c | 150 +
libs/axf/cigar.c | 2578 +++
libs/axf/generate-mismatch-qual.c | 152 +
libs/axf/get-sam-flags.c | 228 +
libs/axf/get_mate_align_ids.c | 332 +
libs/axf/make-cmp-read_desc.c | 176 +
libs/axf/mismatch-restore-qual.c | 135 +
libs/axf/not-my-row.c | 76 +
libs/axf/project_read_from_sequence.c | 285 +
libs/axf/raw-restore-qual.c | 95 +
libs/axf/raw-restore-read.c | 119 +
libs/axf/ref-preserve_qual.c | 429 +
libs/axf/ref-restore-read.c | 201 +
libs/axf/ref-tbl-sub-select.c | 533 +
libs/axf/ref-tbl.c | 106 +
libs/axf/ref-tbl.h | 32 +
libs/axf/refseq-stats.c | 205 +
libs/axf/seq-construct-read.c | 125 +
libs/axf/seq-restore-linkage-group.c | 186 +
libs/axf/seq-restore-read.c | 749 +
libs/axf/template-len.c | 136 +
libs/blast/Makefile | 91 +
libs/blast/blast-mgr.c | 670 +
libs/blast/blast-mgr.h | 78 +
libs/blast/reader.c | 2361 +++
libs/blast/reader.h | 53 +
libs/blast/reference.c | 1710 ++
libs/blast/reference.h | 86 +
libs/blast/run-set.c | 3251 +++
libs/blast/run-set.h | 312 +
libs/cipher/cipher-1.7/PKG-INFO | 13 +
libs/cipher/cipher-1.7/README.md | 4 +
libs/cipher/cipher-1.7/cipher.egg-info/PKG-INFO | 13 +
libs/cipher/cipher-1.7/cipher.egg-info/SOURCES.txt | 12 +
.../cipher.egg-info/dependency_links.txt | 1 +
.../cipher/cipher-1.7/cipher.egg-info/not-zip-safe | 1 +
.../cipher-1.7/cipher.egg-info/top_level.txt | 1 +
libs/cipher/cipher-1.7/cipher/__init__.py | 393 +
libs/cipher/cipher-1.7/decrypt.py | 25 +
libs/cipher/cipher-1.7/encrypt.py | 25 +
libs/cipher/cipher-1.7/requirements-test.txt | 5 +
libs/cipher/cipher-1.7/setup.cfg | 16 +
libs/cipher/cipher-1.7/setup.py | 4 +
libs/csra2/Makefile | 87 +
libs/ext/Makefile | 55 +
libs/ext/bzip2/.gitignore | 4 +
libs/ext/bzip2/LICENSE | 42 +
libs/ext/bzip2/Makefile | 154 +
libs/ext/bzip2/blocksort.c | 1094 +
libs/ext/bzip2/bzip2-1.0.6.diff | 20 +
libs/ext/bzip2/bzip2.c | 2034 ++
libs/ext/bzip2/bzip2recover.c | 514 +
libs/ext/bzip2/bzlib.c | 1572 ++
libs/ext/bzip2/bzlib.h | 282 +
libs/ext/bzip2/bzlib_private.h | 509 +
libs/ext/bzip2/compress.c | 674 +
libs/ext/bzip2/crctable.c | 104 +
libs/ext/bzip2/decompress.c | 646 +
libs/ext/bzip2/dlltest.c | 175 +
libs/ext/bzip2/huffman.c | 205 +
libs/ext/bzip2/mk251.c | 31 +
libs/ext/bzip2/randtable.c | 84 +
libs/ext/bzip2/spewG.c | 54 +
libs/ext/bzip2/unzcrash.c | 141 +
libs/ext/magic/.gitignore | 1 +
libs/ext/magic/Makefile | 127 +
libs/ext/magic/apprentice.c | 2381 +++
libs/ext/magic/apptype.c | 168 +
libs/ext/magic/ascmagic.c | 389 +
libs/ext/magic/asprintf.c | 47 +
libs/ext/magic/cdf.c | 1265 ++
libs/ext/magic/cdf.h | 305 +
libs/ext/magic/cdf_time.c | 192 +
libs/ext/magic/compress.c | 496 +
libs/ext/magic/config.h | 269 +
libs/ext/magic/elfclass.h | 69 +
libs/ext/magic/encoding.c | 500 +
libs/ext/magic/file.c | 482 +
libs/ext/magic/file.h | 457 +
libs/ext/magic/file_opts.h | 49 +
libs/ext/magic/fsmagic.c | 363 +
libs/ext/magic/funcs.c | 426 +
libs/ext/magic/getopt_long.c | 498 +
libs/ext/magic/is_tar.c | 157 +
libs/ext/magic/magic.c | 412 +
libs/ext/magic/mygetopt.h | 68 +
libs/ext/magic/names.h | 173 +
libs/ext/magic/patchlevel.h | 355 +
libs/ext/magic/print.c | 240 +
libs/ext/magic/readcdf.c | 284 +
libs/ext/magic/readelf.c | 1192 ++
libs/ext/magic/readelf.h | 312 +
libs/ext/magic/softmagic.c | 2012 ++
libs/ext/magic/strlcat.c | 58 +
libs/ext/magic/strlcpy.c | 54 +
libs/ext/magic/tar.h | 73 +
libs/ext/magic/vasprintf.c | 642 +
libs/ext/regex/Makefile | 114 +
libs/ext/regex/libregex.def | 18 +
libs/ext/regex/regcomp.c | 3796 ++++
libs/ext/regex/regex.c | 74 +
libs/ext/regex/regex_internal.c | 1717 ++
libs/ext/regex/regex_internal.h | 782 +
libs/ext/regex/regexec.c | 4330 ++++
libs/ext/szip/.gitignore | 4 +
libs/ext/szip/Makefile | 117 +
libs/ext/zlib/.gitignore | 4 +
libs/ext/zlib/Makefile | 162 +
libs/ext/zlib/adler32.c | 179 +
libs/ext/zlib/compress.c | 80 +
libs/ext/zlib/crc32.c | 425 +
libs/ext/zlib/crc32.h | 441 +
libs/ext/zlib/deflate.c | 1967 ++
libs/ext/zlib/deflate.h | 346 +
libs/ext/zlib/gzclose.c | 25 +
libs/ext/zlib/gzguts.h | 213 +
libs/ext/zlib/gzlib.c | 634 +
libs/ext/zlib/gzread.c | 594 +
libs/ext/zlib/gzwrite.c | 577 +
libs/ext/zlib/infback.c | 640 +
libs/ext/zlib/inffast.c | 340 +
libs/ext/zlib/inffast.h | 11 +
libs/ext/zlib/inffixed.h | 94 +
libs/ext/zlib/inflate.c | 1512 ++
libs/ext/zlib/inflate.h | 122 +
libs/ext/zlib/inftrees.c | 306 +
libs/ext/zlib/inftrees.h | 62 +
libs/ext/zlib/sun/stdlib.h | 7 +
libs/ext/zlib/trees.c | 1226 ++
libs/ext/zlib/trees.h | 128 +
libs/ext/zlib/uncompr.c | 59 +
libs/ext/zlib/zconf.h | 511 +
libs/ext/zlib/zlib-1.2.8.diff | 10 +
libs/ext/zlib/zlib.h | 1768 ++
libs/ext/zlib/zutil.c | 324 +
libs/ext/zlib/zutil.h | 253 +
libs/hdf5/.gitignore | 2 +
libs/hdf5/Makefile | 122 +
libs/hdf5/hdf5arrayfile-priv.h | 79 +
libs/hdf5/hdf5arrayfile.c | 656 +
libs/hdf5/hdf5dir.c | 879 +
libs/hdf5/hdf5file.c | 383 +
libs/kapp/Makefile | 152 +
libs/kapp/args-conv.c | 43 +
libs/kapp/args.c | 2380 +++
libs/kapp/args_debug.h | 47 +
libs/kapp/linux/ram.c | 79 +
libs/kapp/loader-file.c | 643 +
libs/kapp/loader-meta.c | 105 +
libs/kapp/log-xml.c | 416 +
libs/kapp/mac/ram.c | 63 +
libs/kapp/main-priv.h | 76 +
libs/kapp/main.c | 516 +
libs/kapp/progressbar.c | 199 +
libs/kapp/queue-file.c | 925 +
libs/kapp/sun/sysmain.c | 243 +
libs/kapp/tokenizer.c | 525 +
libs/kapp/unix/args-conv-os.c | 32 +
libs/kapp/unix/sysmain.c | 296 +
libs/kapp/win/args-conv-os.c | 48 +
libs/kapp/win/main-priv-win.h | 51 +
libs/kapp/win/ram.c | 62 +
libs/kapp/win/sysmain.c | 300 +
.../input/1.0/col/sub1/idx => libs/kdb/.gitignore | 0
libs/kdb/Makefile | 164 +
libs/kdb/btree.c | 579 +
libs/kdb/cc-priv.h | 51 +
libs/kdb/coldata-priv.h | 126 +
libs/kdb/coldata.c | 188 +
libs/kdb/colfmt-priv.h | 339 +
libs/kdb/colidx-priv.h | 122 +
libs/kdb/colidx.c | 243 +
libs/kdb/colidx0-priv.h | 93 +
libs/kdb/colidx0.c | 433 +
libs/kdb/colidx1-priv.h | 130 +
libs/kdb/colidx1.c | 771 +
libs/kdb/colidx2-priv.h | 99 +
libs/kdb/colidx2.c | 219 +
libs/kdb/column-cc.c | 229 +
libs/kdb/column-priv.h | 94 +
libs/kdb/column.c | 1132 ++
libs/kdb/database-cc.c | 339 +
libs/kdb/database-cmn.c | 496 +
libs/kdb/database-priv.h | 115 +
libs/kdb/database.c | 807 +
libs/kdb/dbcc-cmn.c | 141 +
libs/kdb/dbmgr-cmn.c | 485 +
libs/kdb/dbmgr-priv.h | 128 +
libs/kdb/dbmgr.c | 420 +
libs/kdb/idstats-priv.h | 74 +
libs/kdb/idstats.c | 269 +
libs/kdb/idxblk-priv.h | 136 +
libs/kdb/idxblk.c | 695 +
libs/kdb/index-cmn.h | 286 +
libs/kdb/index-priv.h | 134 +
libs/kdb/index.c | 1006 +
libs/kdb/kdb-priv.h | 122 +
libs/kdb/kdb.c | 951 +
libs/kdb/kdbfmt-priv.h | 76 +
libs/kdb/libkdb.vers.h | 27 +
libs/kdb/meta.c | 2141 ++
libs/kdb/ptrieval-v1.c | 265 +
libs/kdb/ptrieval-v2.c | 396 +
libs/kdb/table-cc.c | 378 +
libs/kdb/table-priv.h | 81 +
libs/kdb/table.c | 718 +
libs/kdb/trieidx-priv.h | 74 +
libs/kdb/trieidx-v1.c | 222 +
libs/kdb/trieidx-v2.c | 1047 +
libs/kdb/trieval-v1.c | 49 +
libs/kdb/trieval-v2.c | 49 +
libs/kdb/u64idx-v3.c | 162 +
libs/kdb/wcoldata-priv.h | 172 +
libs/kdb/wcoldata.c | 342 +
libs/kdb/wcolidx-priv.h | 166 +
libs/kdb/wcolidx.c | 694 +
libs/kdb/wcolidx0-priv.h | 153 +
libs/kdb/wcolidx0.c | 831 +
libs/kdb/wcolidx1-priv.h | 152 +
libs/kdb/wcolidx1.c | 921 +
libs/kdb/wcolidx2-priv.h | 114 +
libs/kdb/wcolidx2.c | 241 +
libs/kdb/wcolumn-priv.h | 120 +
libs/kdb/wcolumn.c | 2681 +++
libs/kdb/wdatabase-priv.h | 95 +
libs/kdb/wdatabase.c | 1642 ++
libs/kdb/wdbmgr.c | 421 +
libs/kdb/werror-priv.h | 59 +
libs/kdb/widxblk-priv.h | 195 +
libs/kdb/widxblk.c | 546 +
libs/kdb/windex-priv.h | 230 +
libs/kdb/windex.c | 1889 ++
libs/kdb/wkdb-priv.h | 160 +
libs/kdb/wkdb.c | 1430 ++
libs/kdb/wmeta.c | 3526 ++++
libs/kdb/wtable-priv.h | 106 +
libs/kdb/wtable.c | 1638 ++
libs/kdb/wtrieidx-v1.c | 1100 +
libs/kdb/wtrieidx-v2.c | 2560 +++
libs/kdb/wu64idx-v3.c | 416 +
libs/kfc/Makefile | 97 +
libs/kfc/except.c | 128 +
libs/kfc/refcount.c | 180 +
libs/kfc/rsrc-priv.h | 44 +
libs/kfc/rsrc.c | 180 +
libs/kfc/sysctx-priv.h | 45 +
libs/kfc/tstate.c | 1041 +
libs/kfc/unix/sysctx.c | 192 +
libs/kfc/unix/sysrsrc.c | 148 +
libs/kfc/vtbl.c | 205 +
libs/kfc/win/sysctx.c | 342 +
libs/kfc/win/sysrsrc.c | 186 +
libs/kfc/xc.c | 36 +
libs/kfg/.gitignore | 2 +
libs/kfg/Makefile | 126 +
libs/kfg/config-aws.c | 315 +
libs/kfg/config-grammar.c | 1726 ++
libs/kfg/config-grammar.y | 185 +
libs/kfg/config-lex.c | 2517 +++
libs/kfg/config-lex.l | 221 +
libs/kfg/config-tokens.h | 75 +
libs/kfg/config.c | 4368 ++++
libs/kfg/default.kfg | 53 +
libs/kfg/kart.c | 720 +
libs/kfg/keystore.c | 858 +
libs/kfg/kfg-lex.h | 67 +
libs/kfg/kfg-parse.h | 41 +
libs/kfg/kfg-priv.h | 32 +
libs/kfg/ngc-priv.h | 59 +
libs/kfg/ngc.c | 484 +
libs/kfg/properties.c | 721 +
libs/kfg/report-kfg.c | 532 +
libs/kfg/repository.c | 1972 ++
libs/kfs/.gitignore | 1 +
libs/kfs/Makefile | 221 +
libs/kfs/arc.c | 4089 ++++
libs/kfs/arrayfile.c | 423 +
libs/kfs/buffile-read.c | 265 +
libs/kfs/buffile-write.c | 371 +
libs/kfs/buffile.c | 574 +
libs/kfs/bzip.c | 836 +
libs/kfs/cacheteefile.c | 1833 ++
libs/kfs/countfile.c | 652 +
libs/kfs/crc32.c | 1771 ++
libs/kfs/dir_test.c | 54 +
libs/kfs/directory-v2.c | 1185 ++
libs/kfs/directory.c | 1539 ++
libs/kfs/extendable-ramfile.c | 280 +
libs/kfs/ffext.c | 812 +
libs/kfs/ffkey.c | 833 +
libs/kfs/ffmagic.c | 969 +
libs/kfs/file-v2.c | 724 +
libs/kfs/file.c | 1002 +
libs/kfs/fileformat-priv.h | 124 +
libs/kfs/fileformat.c | 291 +
libs/kfs/from_to_namelist.c | 454 +
libs/kfs/gzip.c | 646 +
libs/kfs/impl.h | 120 +
libs/kfs/karc-priv.h | 43 +
libs/kfs/kfs-priv.h | 47 +
libs/kfs/kfsmagic | 20101 +++++++++++++++++++
libs/kfs/lockfile.c | 350 +
libs/kfs/manager.c | 641 +
libs/kfs/md5.c | 1910 ++
libs/kfs/mmap-priv.h | 111 +
libs/kfs/mmap.c | 754 +
libs/kfs/nullfile.c | 273 +
libs/kfs/pagefile.c | 1388 ++
libs/kfs/pmem.c | 632 +
libs/kfs/quickmount.c | 967 +
libs/kfs/ramfile.c | 424 +
libs/kfs/readheadfile.c | 294 +
libs/kfs/report.c | 169 +
libs/kfs/sra.c | 486 +
libs/kfs/subfile.c | 337 +
libs/kfs/szip.c | 575 +
libs/kfs/tar.c | 2672 +++
libs/kfs/teefile.c | 532 +
libs/kfs/toc-priv.h | 841 +
libs/kfs/toc.c | 1764 ++
libs/kfs/tocdir.c | 411 +
libs/kfs/tocentry.c | 1748 ++
libs/kfs/tocfile.c | 635 +
libs/kfs/unix/sysdir-priv.h | 68 +
libs/kfs/unix/sysdir.c | 2414 +++
libs/kfs/unix/sysdll.c | 1436 ++
libs/kfs/unix/sysfile-priv.h | 89 +
libs/kfs/unix/sysfile-v2.c | 1018 +
libs/kfs/unix/sysfile.c | 1079 +
libs/kfs/unix/syslockfile.c | 215 +
libs/kfs/unix/sysmmap-priv.h | 68 +
libs/kfs/unix/sysmmap.c | 143 +
libs/kfs/win/directory-path.c | 83 +
libs/kfs/win/lnk_tools.c | 518 +
libs/kfs/win/sysdir-priv.h | 92 +
libs/kfs/win/sysdir.c | 3135 +++
libs/kfs/win/sysdll.c | 1417 ++
libs/kfs/win/sysfile-priv.h | 82 +
libs/kfs/win/sysfile-v2.c | 1028 +
libs/kfs/win/sysfile.c | 1059 +
libs/kfs/win/syslockfile.c | 67 +
libs/kfs/win/sysmmap-priv.h | 71 +
libs/kfs/win/sysmmap.c | 138 +
libs/klib/.gitignore | 1 +
libs/klib/Judy.h | 635 +
libs/klib/Makefile | 159 +
libs/klib/SHA-32bit.c | 313 +
libs/klib/SHA-64bit.c | 271 +
libs/klib/bsd/syserrcode.c | 44 +
libs/klib/bsearch.c | 77 +
libs/klib/bstpersist.c | 252 +
libs/klib/btree.c | 1458 ++
libs/klib/container.c | 1646 ++
libs/klib/cp1252.c | 65 +
libs/klib/crc32.c | 500 +
libs/klib/data-buffer.c | 656 +
libs/klib/debug.c | 352 +
libs/klib/iso8859-1.c | 42 +
libs/klib/iso8859.c | 205 +
libs/klib/judy-vector.c | 1793 ++
.../1.0/col/sub1/idx0 => libs/klib/judy/.gitignore | 0
libs/klib/judy/Judy1.h | 549 +
libs/klib/judy/Judy1Tables.32.c | 72 +
libs/klib/judy/Judy1Tables.64.c | 132 +
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/JudyLTables.32.c | 121 +
libs/klib/judy/JudyLTables.64.c | 219 +
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/Judy_Bit.c | 23 +
libs/klib/judy/Judy_Bit_Cascade.c | 3 +
libs/klib/judy/Judy_Bit_Count.c | 3 +
libs/klib/judy/Judy_Bit_Decascade.c | 3 +
libs/klib/judy/Judy_Bit_Next.c | 3 +
libs/klib/judy/Judy_Bit_NextEmpty.c | 3 +
libs/klib/judy/Judy_Bit_Prev.c | 3 +
libs/klib/judy/Judy_Word.c | 23 +
libs/klib/judy/Judy_Word_Cascade.c | 3 +
libs/klib/judy/Judy_Word_Count.c | 3 +
libs/klib/judy/Judy_Word_Decascade.c | 3 +
libs/klib/judy/Judy_Word_Next.c | 3 +
libs/klib/judy/Judy_Word_NextEmpty.c | 3 +
libs/klib/judy/Judy_Word_Prev.c | 3 +
libs/klib/judy/Makefile | 225 +
libs/klib/judy/_Judy1Tables.c | 31 +
libs/klib/judy/_JudyLTables.c | 31 +
libs/klib/judy/j__udyGet.c | 2 +
libs/klib/ksort.c | 98 +
libs/klib/linux/syserrcode.c | 53 +
libs/klib/log-priv.h | 96 +
libs/klib/log.c | 986 +
libs/klib/maybeswap.h | 57 +
libs/klib/md5.c | 421 +
libs/klib/namelist.c | 149 +
libs/klib/ncbi-vdb-version.c | 45 +
libs/klib/num-gen.c | 1157 ++
libs/klib/out.c | 208 +
libs/klib/pack.c | 517 +
libs/klib/pbstree-impl.c | 847 +
libs/klib/pbstree-native.c | 30 +
libs/klib/pbstree-priv.h | 680 +
libs/klib/pbstree-swapped.c | 30 +
libs/klib/pbstree.c | 395 +
libs/klib/printf.c | 3540 ++++
libs/klib/progressbar.c | 160 +
libs/klib/ptpersist.c | 1121 ++
libs/klib/ptrie.c | 1992 ++
libs/klib/qsort.c | 311 +
libs/klib/rc-idx-tbl.c | 39 +
libs/klib/rc-tbl.c | 36 +
libs/klib/refcount.c | 499 +
libs/klib/release-vers.h | 42 +
libs/klib/report-klib.c | 908 +
libs/klib/sra-release-version.c | 329 +
libs/klib/status-rc-strings.c | 39 +
libs/klib/status-rc.c | 156 +
libs/klib/status.c | 436 +
libs/klib/sun/syslog.c | 208 +
libs/klib/sun/systime.c | 110 +
libs/klib/symtab.c | 736 +
libs/klib/text.c | 1099 +
libs/klib/time.c | 3 +
libs/klib/token.c | 1291 ++
libs/klib/trie-priv.h | 237 +
libs/klib/trie.c | 1486 ++
libs/klib/trieval.c | 168 +
libs/klib/unix/misc.c | 33 +
libs/klib/unix/syserrcode.c | 46 +
libs/klib/unix/syslog.c | 209 +
libs/klib/unix/systime.c | 162 +
libs/klib/unix/syswriter.c | 163 +
libs/klib/unpack.c | 833 +
libs/klib/utf8.c | 1355 ++
libs/klib/vector.c | 626 +
libs/klib/vector_namelist.c | 633 +
libs/klib/vlen-encode.c | 773 +
libs/klib/win/misc.c | 33 +
libs/klib/win/sysalloc.c | 68 +
libs/klib/win/syserrcode.c | 85 +
libs/klib/win/syslog.c | 121 +
libs/klib/win/systime.c | 355 +
libs/klib/win/syswriter.c | 185 +
libs/klib/writer-priv.h | 169 +
libs/klib/writer.c | 644 +
libs/kns/Makefile | 115 +
libs/kns/buffered-stream.c | 249 +
libs/kns/endpoint.c | 155 +
libs/kns/http-client.c | 3095 +++
libs/kns/http-file.c | 639 +
libs/kns/http-priv.h | 150 +
libs/kns/http-retrier.c | 503 +
libs/kns/http.c | 324 +
libs/kns/kns_manager-ext.c | 157 +
libs/kns/kns_manager.c | 346 +
libs/kns/linux/sysendpoint.c | 158 +
libs/kns/linux/syspoll.c | 107 +
libs/kns/mac/sysendpoint.c | 140 +
libs/kns/mac/syspoll.c | 96 +
libs/kns/manager.c | 720 +
libs/kns/mgr-priv.h | 87 +
libs/kns/poll-priv.h | 51 +
libs/kns/stream-from-files.c | 168 +
libs/kns/stream-from-streams.c | 150 +
libs/kns/stream-priv.h | 40 +
libs/kns/stream.c | 782 +
libs/kns/sysmgr.h | 41 +
libs/kns/unix/sysmgr.c | 37 +
libs/kns/unix/syssock.c | 1188 ++
libs/kns/unix/sysstream.c | 251 +
libs/kns/url-fetcher-curl.c | 255 +
libs/kns/url-fetcher-impl.h | 109 +
libs/kns/url-fetcher.c | 129 +
libs/kns/win/sysendpoint.c | 147 +
libs/kns/win/sysmgr.c | 65 +
libs/kns/win/syssock.c | 1855 ++
libs/kns/win/sysstream.c | 232 +
libs/kproc/Makefile | 162 +
libs/kproc/bsd/syslock-priv.h | 72 +
libs/kproc/bsd/syslock.c | 932 +
libs/kproc/bsd/sysmgr.c | 38 +
libs/kproc/linux/sysbarrier.c | 170 +
libs/kproc/linux/syslock-priv.h | 68 +
libs/kproc/linux/syslock.c | 617 +
libs/kproc/linux/sysmgr.c | 52 +
libs/kproc/procmgr.c | 412 +
libs/kproc/queue.c | 428 +
libs/kproc/sem.c | 472 +
libs/kproc/stbarrier.c | 128 +
libs/kproc/stcond.c | 152 +
libs/kproc/stlock.c | 311 +
libs/kproc/stsem.c | 233 +
libs/kproc/stthread.c | 149 +
libs/kproc/sttimeout.c | 65 +
libs/kproc/sun/sysbarrier.c | 170 +
libs/kproc/sun/syslock-priv.h | 62 +
libs/kproc/sun/syslock.c | 501 +
libs/kproc/task.c | 156 +
libs/kproc/unix/syscond-priv.h | 78 +
libs/kproc/unix/syscond.c | 320 +
libs/kproc/unix/systhread.c | 272 +
libs/kproc/unix/systimeout.c | 86 +
libs/kproc/win/syscond-priv.h | 79 +
libs/kproc/win/syscond.c | 500 +
libs/kproc/win/syslock-priv.h | 67 +
libs/kproc/win/syslock.c | 725 +
libs/kproc/win/sysmgr.c | 37 +
libs/kproc/win/systhread.c | 291 +
libs/kproc/win/systimeout.c | 70 +
libs/krypto/.gitignore | 2 +
libs/krypto/Makefile | 297 +
libs/krypto/aes-byte.c | 236 +
libs/krypto/aes-impl.c | 1 +
libs/krypto/aes-ncbi-ni.c | 2 +
libs/krypto/aes-ncbi-priv.h | 227 +
libs/krypto/aes-ncbi.c | 2641 +++
libs/krypto/aes-priv.h | 94 +
libs/krypto/aes.c | 1 +
libs/krypto/aes_core.c | 1181 ++
libs/krypto/aes_x86core.c | 2 +
libs/krypto/aesx86.c | 1 +
libs/krypto/blockcipher-byte-impl.h | 113 +
libs/krypto/blockcipher-impl.h | 187 +
libs/krypto/blockcipher-priv.h | 90 +
libs/krypto/blockcipher-vec-impl.h | 119 +
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.c | 808 +
libs/krypto/cipher.c | 543 +
libs/krypto/ciphermgr.c | 295 +
libs/krypto/ciphertest.c | 80 +
libs/krypto/compile-test.c | 50 +
libs/krypto/csprng.c | 163 +
libs/krypto/encfile-priv.h | 162 +
libs/krypto/encfile.c | 2019 ++
libs/krypto/encfilev2.c | 2621 +++
libs/krypto/key.c | 126 +
libs/krypto/manager.c | 11 +
libs/krypto/ncbi-priv.h | 122 +
libs/krypto/no-null-ncbi.c | 59 +
libs/krypto/null-ncbi-priv.h | 56 +
libs/krypto/null-ncbi.c | 251 +
libs/krypto/reencfile.c | 1243 ++
libs/krypto/rng-impl.h | 91 +
.../1.0/col/sub1/idx1 => libs/krypto/rng-priv.h | 0
libs/krypto/rng.c | 120 +
libs/krypto/testcipher.c | 76 +
libs/krypto/unix/sysrng.c | 114 +
libs/krypto/wgaencrypt.c | 1254 ++
libs/krypto/win/sysrng.c | 132 +
libs/ktst/Makefile | 87 +
libs/ktst/testcase.cpp | 108 +
libs/ktst/testenv.cpp | 518 +
libs/ktst/testrunner.cpp | 86 +
libs/ktst/unix/systestenv.cpp | 137 +
libs/ktst/win/systestenv.cpp | 167 +
libs/kxml/Makefile | 117 +
libs/kxml/xml.c | 1705 ++
libs/kxml/xtoc-parsexml.c | 576 +
libs/kxml/xtoc-priv.h | 124 +
libs/kxml/xtoc.c | 3464 ++++
libs/loader/Makefile | 88 +
libs/loader/alignment-writer.c | 271 +
libs/loader/common-reader.c | 614 +
libs/loader/common-writer.c | 2067 ++
libs/loader/mmarray.c | 131 +
libs/loader/reference-writer.c | 483 +
libs/loader/sequence-writer.c | 366 +
libs/ncbi-vdb/Makefile | 157 +
libs/ncbi-vdb/libncbi-vdb.vers | 1 +
libs/ngs-c++/Makefile | 103 +
libs/ngs-c++/NCBI-NGS.cpp | 106 +
libs/ngs-c++/testy-the-bear.cpp | 277 +
libs/ngs-jni/.gitignore | 1 +
libs/ngs-jni/Makefile | 109 +
libs/ngs-jni/jni.h | 1944 ++
libs/ngs-jni/jni_ErrorMsg.c | 173 +
libs/ngs-jni/jni_ErrorMsg.h | 89 +
libs/ngs-jni/jni_Manager.c | 250 +
libs/ngs-jni/jni_Manager.h | 77 +
libs/ngs-jni/jni_String.c | 193 +
libs/ngs-jni/jni_String.h | 91 +
libs/ngs-jni/jni_md.h | 28 +
libs/ngs-py/Makefile | 87 +
libs/ngs-py/py_Manager.c | 218 +
libs/ngs-py/py_Manager.h | 27 +
libs/ngs-py/py_ngs_defs.h | 15 +
libs/ngs/BAM_Alignment.c | 641 +
libs/ngs/BAM_Alignment.h | 58 +
libs/ngs/BAM_ReadCollection.c | 1522 ++
libs/ngs/BAM_Record.c | 142 +
libs/ngs/BAM_Record.h | 82 +
libs/ngs/CSRA1_Alignment.c | 1430 ++
libs/ngs/CSRA1_Alignment.h | 83 +
libs/ngs/CSRA1_Pileup.c | 1921 ++
libs/ngs/CSRA1_Pileup.h | 341 +
libs/ngs/CSRA1_PileupEvent.c | 931 +
libs/ngs/CSRA1_PileupEvent.h | 50 +
libs/ngs/CSRA1_Read.c | 496 +
libs/ngs/CSRA1_Read.h | 96 +
libs/ngs/CSRA1_ReadCollection.c | 753 +
libs/ngs/CSRA1_ReadCollection.h | 58 +
libs/ngs/CSRA1_Reference.c | 1068 +
libs/ngs/CSRA1_Reference.h | 96 +
libs/ngs/CSRA1_ReferenceWindow.c | 1049 +
libs/ngs/CSRA1_ReferenceWindow.h | 67 +
libs/ngs/EBI_ReferenceSequence.c | 408 +
libs/ngs/EBI_ReferenceSequence.h | 51 +
libs/ngs/Makefile | 128 +
libs/ngs/Model.graphml | 661 +
libs/ngs/NCBI-NGS.c | 66 +
libs/ngs/NCBI-NGS.h | 58 +
libs/ngs/NGS_Alignment.c | 978 +
libs/ngs/NGS_Alignment.h | 206 +
libs/ngs/NGS_Cursor.c | 575 +
libs/ngs/NGS_Cursor.h | 134 +
libs/ngs/NGS_ErrBlock.c | 57 +
libs/ngs/NGS_ErrBlock.h | 53 +
libs/ngs/NGS_Fragment.c | 286 +
libs/ngs/NGS_Fragment.h | 175 +
libs/ngs/NGS_FragmentBlob.c | 476 +
libs/ngs/NGS_FragmentBlob.h | 125 +
libs/ngs/NGS_FragmentBlobIterator.c | 185 +
libs/ngs/NGS_FragmentBlobIterator.h | 79 +
libs/ngs/NGS_Id.c | 179 +
libs/ngs/NGS_Id.h | 93 +
libs/ngs/NGS_Pileup.c | 235 +
libs/ngs/NGS_Pileup.h | 147 +
libs/ngs/NGS_PileupEvent.c | 493 +
libs/ngs/NGS_PileupEvent.h | 179 +
libs/ngs/NGS_Read.c | 522 +
libs/ngs/NGS_Read.h | 190 +
libs/ngs/NGS_ReadCollection.c | 674 +
libs/ngs/NGS_ReadCollection.h | 194 +
libs/ngs/NGS_ReadGroup.c | 229 +
libs/ngs/NGS_ReadGroup.h | 127 +
libs/ngs/NGS_Refcount.c | 182 +
libs/ngs/NGS_Refcount.h | 102 +
libs/ngs/NGS_Reference.c | 916 +
libs/ngs/NGS_Reference.h | 214 +
libs/ngs/NGS_ReferenceSequence.c | 282 +
libs/ngs/NGS_ReferenceSequence.h | 138 +
libs/ngs/NGS_Statistics.c | 335 +
libs/ngs/NGS_Statistics.h | 143 +
libs/ngs/NGS_String.c | 413 +
libs/ngs/NGS_String.h | 109 +
libs/ngs/NOTES.txt | 128 +
libs/ngs/SRA_DB_ReadCollection.c | 456 +
libs/ngs/SRA_Read.c | 936 +
libs/ngs/SRA_Read.h | 169 +
libs/ngs/SRA_ReadCollection.c | 424 +
libs/ngs/SRA_ReadGroup.c | 429 +
libs/ngs/SRA_ReadGroup.h | 73 +
libs/ngs/SRA_ReadGroupInfo.c | 333 +
libs/ngs/SRA_ReadGroupInfo.h | 89 +
libs/ngs/SRA_ReferenceSequence.c | 374 +
libs/ngs/SRA_ReferenceSequence.h | 56 +
libs/ngs/SRA_Statistics.c | 773 +
libs/ngs/SRA_Statistics.h | 61 +
libs/ngs/extern.h | 41 +
.../1.0/col/sub1/idx2 => libs/search/.gitignore | 0
libs/search/Makefile | 98 +
libs/search/agrep-dp.c | 880 +
libs/search/agrep-myers.c | 644 +
libs/search/agrep-myersunltd.c | 1039 +
libs/search/agrep-wumanber.c | 415 +
libs/search/debug.h | 43 +
libs/search/fgrep-aho.c | 363 +
libs/search/fgrep-boyermoore.c | 462 +
libs/search/fgrep-dumb.c | 326 +
libs/search/nucstrstr.c | 4621 +++++
libs/search/search-priv.h | 140 +
libs/search/search.c | 388 +
libs/search/sw-search.c | 1496 ++
libs/sra/.gitignore | 1 +
libs/sra/Makefile | 249 +
libs/sra/built-in.vschema | 580 +
libs/sra/libsra-schema.vers.h | 27 +
libs/sra/libsradb.vers.h | 27 +
libs/sra/libsrareader.vers.h | 1 +
libs/sra/libsraschema.vers.h | 1 +
libs/sra/libwsradb.vers.h | 1 +
libs/sra/libwsraschema.vers.h | 1 +
libs/sra/reader-abi.c | 473 +
libs/sra/reader-cmn.c | 379 +
libs/sra/reader-cmn.h | 161 +
libs/sra/reader-fastq.c | 623 +
libs/sra/reader-illumina.c | 567 +
libs/sra/reader-sff.c | 380 +
libs/sra/sra-debug.h | 42 +
libs/sra/sra-dflt-schema.c | 552 +
libs/sra/sra-priv.h | 183 +
libs/sra/sra-schema.c | 4133 ++++
libs/sra/sracache.c | 560 +
libs/sra/sracol.c | 235 +
libs/sra/sramgr-cmn.c | 572 +
libs/sra/sramgr.c | 186 +
libs/sra/sraschema-priv.h | 36 +
libs/sra/sraschema-stub.c | 51 +
libs/sra/sraschema.c | 74 +
libs/sra/sratbl-cmn.c | 1458 ++
libs/sra/sratbl.c | 118 +
libs/sra/types.c | 298 +
libs/sra/wsramgr.c | 165 +
libs/sra/wsraschema-stub.c | 51 +
libs/sra/wsratbl.c | 649 +
libs/sraxf/.gitignore | 1 +
libs/sraxf/Makefile | 152 +
libs/sraxf/bio-start.c | 197 +
libs/sraxf/color-from-dna.c | 151 +
libs/sraxf/denormalize.c | 231 +
libs/sraxf/dna-from-color.c | 150 +
libs/sraxf/dynamic-454-read-descriptor.c | 303 +
libs/sraxf/extract-coordinates.c | 354 +
libs/sraxf/extract-name_coord.c | 243 +
libs/sraxf/extract-name_fmt.c | 240 +
libs/sraxf/extract-spot_name.c | 105 +
libs/sraxf/fix_read_seg_impl.h | 169 +
libs/sraxf/format-spot-name.c | 333 +
libs/sraxf/fpcodec.c | 267 +
libs/sraxf/index_lookup.c | 270 +
libs/sraxf/make-position.c | 133 +
libs/sraxf/name-tokenizer.h | 121 +
libs/sraxf/normalize.c | 240 +
libs/sraxf/prefix-tree-to-name.c | 162 +
libs/sraxf/process-position.c | 198 +
libs/sraxf/qstat-trigger.c | 256 +
libs/sraxf/qual4_codec.h | 43 +
libs/sraxf/qual4_decode.c | 257 +
libs/sraxf/qual4_encode.c | 232 +
libs/sraxf/read-desc.c | 143 +
libs/sraxf/read-seg-from-readn.c | 361 +
libs/sraxf/rewrite-spot-name.c | 223 +
libs/sraxf/rotate.c | 271 +
libs/sraxf/spot-desc.c | 102 +
libs/sraxf/stat_mod.c | 392 +
libs/sraxf/stat_mod.h | 80 +
libs/sraxf/stats.c | 764 +
libs/sraxf/stats_quality.c | 132 +
libs/sraxf/swap.c | 228 +
libs/sraxf/tokenize-spot_name-454.c | 122 +
libs/sraxf/tokenize-spot_name-abi.c | 146 +
libs/sraxf/tokenize-spot_name-generic-fastq.c | 82 +
libs/sraxf/tokenize-spot_name-helicos.c | 112 +
libs/sraxf/tokenize-spot_name-illumina.c | 151 +
libs/sraxf/tokenize-spot_name-ion-torrent.c | 136 +
libs/sraxf/untyped-priv.h | 83 +
libs/sraxf/untyped.c | 378 +
libs/sraxf/v0-decompress-init.c | 2838 +++
libs/sraxf/v0-decompress-local.h | 368 +
libs/sraxf/v0-decompress.c | 1093 +
libs/sraxf/v0-decompress.h | 170 +
libs/sraxf/v0-funcs.c | 337 +
libs/sraxf/varloc.c | 105 +
tools/sra/.cvsignore => libs/svdb/.gitignore | 0
libs/svdb/Makefile | 95 +
libs/svdb/svdb.c | 3215 +++
libs/tui/Makefile | 137 +
libs/tui/bsd/systui.c | 619 +
libs/tui/dir_dlg.c | 470 +
libs/tui/eventring.c | 134 +
libs/tui/eventring.h | 74 +
libs/tui/file_dlg.c | 380 +
libs/tui/line_policy.c | 379 +
libs/tui/line_policy.h | 86 +
libs/tui/linux/systui.c | 624 +
libs/tui/screen.c | 209 +
libs/tui/screen.h | 75 +
libs/tui/string_cache.c | 378 +
libs/tui/string_cache.h | 54 +
libs/tui/tui-priv.h | 87 +
libs/tui/tui.c | 380 +
libs/tui/tui_cpp.cpp | 226 +
libs/tui/tui_dlg.c | 1291 ++
libs/tui/tui_dlg_helper.c | 250 +
libs/tui/tui_menu.c | 913 +
libs/tui/tui_menu.h | 49 +
libs/tui/tui_palette.c | 304 +
libs/tui/tui_std_dlg.c | 355 +
libs/tui/tui_widget.c | 1079 +
libs/tui/tui_widget.h | 210 +
libs/tui/tui_widget_button.c | 87 +
libs/tui/tui_widget_checkbox.c | 87 +
libs/tui/tui_widget_grid.c | 488 +
libs/tui/tui_widget_inputline.c | 181 +
libs/tui/tui_widget_label.c | 53 +
libs/tui/tui_widget_progress.c | 120 +
libs/tui/tui_widget_radiobox.c | 130 +
libs/tui/tui_widget_spin_edit.c | 118 +
libs/tui/tui_widget_string_list.c | 183 +
libs/tui/unix/systui.c | 29 +
libs/tui/win/systui.c | 590 +
libs/vdb/.gitignore | 1 +
libs/vdb/Makefile | 188 +
libs/vdb/blob-headers.c | 726 +
libs/vdb/blob-headers.h | 114 +
libs/vdb/blob-priv.h | 206 +
libs/vdb/blob.c | 1690 ++
libs/vdb/blob.h | 84 +
libs/vdb/cast.c | 583 +
libs/vdb/column-cmn.c | 356 +
libs/vdb/column-priv.h | 304 +
libs/vdb/column.c | 80 +
libs/vdb/compare.c | 242 +
libs/vdb/cursor-cmn.c | 2910 +++
libs/vdb/cursor-priv.h | 322 +
libs/vdb/cursor.c | 200 +
libs/vdb/database-cmn.c | 928 +
libs/vdb/database-depend.c | 1807 ++
libs/vdb/database-load.c | 119 +
libs/vdb/database-priv.h | 150 +
libs/vdb/database.c | 29 +
libs/vdb/dbmgr-cmn.c | 917 +
libs/vdb/dbmgr-priv.h | 115 +
libs/vdb/dbmgr.c | 157 +
libs/vdb/delta_average.c | 298 +
libs/vdb/environment-read.c | 108 +
libs/vdb/fixed-row-len.c | 67 +
libs/vdb/gen-cast.pl | 480 +
libs/vdb/index_insert.c | 150 +
libs/vdb/index_lookup.c | 191 +
libs/vdb/index_project.c | 221 +
libs/vdb/libvdb.vers.h | 27 +
libs/vdb/linker-cmn.c | 656 +
libs/vdb/linker-int.c | 679 +
libs/vdb/linker-priv.h | 272 +
libs/vdb/linker.c | 45 +
libs/vdb/merge.c | 215 +
libs/vdb/meta-append.c | 145 +
libs/vdb/meta-attr-read.c | 448 +
libs/vdb/meta-attr-write.c | 529 +
libs/vdb/meta-read.c | 140 +
libs/vdb/meta-value.c | 381 +
libs/vdb/meta-write.c | 155 +
libs/vdb/page-map.c | 1734 ++
libs/vdb/page-map.h | 386 +
libs/vdb/parameter-read.c | 103 +
libs/vdb/phys-cmn.c | 784 +
libs/vdb/phys-load.c | 330 +
libs/vdb/phys-priv.h | 194 +
libs/vdb/phys.c | 67 +
libs/vdb/prod-cmn.c | 2506 +++
libs/vdb/prod-expr.c | 885 +
libs/vdb/prod-expr.h | 202 +
libs/vdb/prod-func.c | 957 +
libs/vdb/prod-priv.h | 462 +
libs/vdb/prod.c | 136 +
libs/vdb/range-validate.c | 195 +
libs/vdb/redimension.c | 108 +
libs/vdb/report-vdb.c | 853 +
libs/vdb/row-id.c | 64 +
libs/vdb/row-len.c | 65 +
libs/vdb/schema-db.c | 752 +
libs/vdb/schema-dump.c | 683 +
libs/vdb/schema-dump.h | 208 +
libs/vdb/schema-eval.c | 1400 ++
libs/vdb/schema-expr.c | 2170 ++
libs/vdb/schema-expr.h | 396 +
libs/vdb/schema-func.c | 1657 ++
libs/vdb/schema-int.c | 376 +
libs/vdb/schema-parse.c | 857 +
libs/vdb/schema-parse.h | 607 +
libs/vdb/schema-priv.h | 1308 ++
libs/vdb/schema-prod.c | 1004 +
libs/vdb/schema-tbl.c | 2925 +++
libs/vdb/schema-tok.c | 74 +
libs/vdb/schema-tok.h | 61 +
libs/vdb/schema-type.c | 2573 +++
libs/vdb/schema.c | 1768 ++
libs/vdb/split.c | 398 +
libs/vdb/table-cmn.c | 1401 ++
libs/vdb/table-load.c | 323 +
libs/vdb/table-priv.h | 238 +
libs/vdb/table.c | 109 +
libs/vdb/transpose.c | 720 +
libs/vdb/wcolumn.c | 1074 +
libs/vdb/wcursor.c | 1238 ++
libs/vdb/wdatabase.c | 680 +
libs/vdb/wdbmgr.c | 267 +
libs/vdb/wlinker.c | 98 +
libs/vdb/wphys.c | 912 +
libs/vdb/wprod.c | 439 +
libs/vdb/wtable.c | 1055 +
libs/vdb/xform-priv.h | 83 +
libs/vfs/Makefile | 102 +
libs/vfs/keyring.c | 292 +
libs/vfs/keyring.h | 111 +
libs/vfs/kurl-stub.c | 18 +
libs/vfs/manager.c | 3326 +++
libs/vfs/path-priv.h | 147 +
libs/vfs/path.c | 3788 ++++
libs/vfs/resolver-3.0.c | 326 +
libs/vfs/resolver-priv.h | 241 +
libs/vfs/resolver.c | 4673 +++++
libs/vfs/srapath-stub.c | 372 +
libs/vfs/srapath.c | 1424 ++
libs/vfs/unix/syskeyring.c | 161 +
libs/vfs/unix/syspath.c | 155 +
libs/vfs/win/syskeyring.c | 58 +
libs/vfs/win/syspath.c | 471 +
libs/vxf/.gitignore | 1 +
libs/vxf/Makefile | 196 +
libs/vxf/add-row-id.c | 80 +
libs/vxf/bit_or.c | 135 +
libs/vxf/bunzip.c | 130 +
libs/vxf/bzip.c | 184 +
libs/vxf/ceil.c | 48 +
libs/vxf/checksum.c | 566 +
libs/vxf/clip.c | 200 +
libs/vxf/cut.c | 227 +
libs/vxf/delta.c | 108 +
libs/vxf/deriv.c | 109 +
libs/vxf/diff.c | 356 +
libs/vxf/echo.c | 187 +
libs/vxf/entrez.c | 170 +
libs/vxf/exists.c | 212 +
libs/vxf/extract_token.c | 105 +
libs/vxf/floor.c | 49 +
libs/vxf/fsplit-join.impl.h | 136 +
libs/vxf/funzip.c | 172 +
libs/vxf/fzip.c | 168 +
libs/vxf/integral.c | 113 +
libs/vxf/integral_0.c | 113 +
libs/vxf/irzip.c | 564 +
libs/vxf/irzip.impl.h | 482 +
libs/vxf/iunzip.c | 748 +
libs/vxf/izip-common.h | 195 +
libs/vxf/izip-decode.impl.h | 162 +
libs/vxf/izip-encode.impl.h | 523 +
libs/vxf/izip.c | 866 +
libs/vxf/lower-case-tech-reads.c | 111 +
libs/vxf/map.c | 1017 +
libs/vxf/math-funcs-impl.h | 361 +
libs/vxf/max.c | 175 +
libs/vxf/min.c | 175 +
libs/vxf/outlier-decoder.c | 113 +
libs/vxf/outlier-encoder.c | 141 +
libs/vxf/pack.c | 92 +
libs/vxf/paste.c | 357 +
libs/vxf/rand_4na_2na.c | 200 +
libs/vxf/rldecode.c | 155 +
libs/vxf/rlencode.c | 262 +
libs/vxf/round.c | 49 +
libs/vxf/simple-sub-select.c | 293 +
libs/vxf/sprintf.c | 1280 ++
libs/vxf/strtonum.c | 354 +
libs/vxf/subtract-row-id.c | 83 +
libs/vxf/sum.c | 356 +
libs/vxf/trim.c | 229 +
libs/vxf/trunc.c | 49 +
libs/vxf/undelta.c | 108 +
libs/vxf/unpack.c | 115 +
libs/vxf/unzip.c | 234 +
libs/vxf/vec-sum.c | 239 +
libs/vxf/wgs-tokenize-accession.c | 213 +
libs/vxf/zip.c | 216 +
libs/wgsxf/Makefile | 127 +
libs/wgsxf/build_read_type.c | 113 +
libs/wgsxf/build_scaffold.c | 435 +
libs/xfs/Makefile | 140 +
libs/xfs/bogus.c | 373 +
libs/xfs/common.h | 217 +
libs/xfs/contnode.c | 685 +
libs/xfs/contnode.h | 98 +
libs/xfs/doc.c | 730 +
libs/xfs/docnode.c | 745 +
libs/xfs/editors.c | 491 +
libs/xfs/encro.c | 875 +
libs/xfs/encws.c | 1793 ++
libs/xfs/foo.c | 250 +
libs/xfs/gap.c | 585 +
libs/xfs/gapc.c | 993 +
libs/xfs/gapf.c | 879 +
libs/xfs/gapk.c | 440 +
libs/xfs/gapka.c | 1005 +
libs/xfs/gapks.c | 882 +
libs/xfs/handle.c | 227 +
libs/xfs/http.c | 1300 ++
libs/xfs/kfs.c | 2038 ++
libs/xfs/lockdpt.c | 192 +
libs/xfs/lockdpt.h | 76 +
libs/xfs/lreader.c | 459 +
libs/xfs/lreader.h | 117 +
libs/xfs/mehr.c | 258 +
libs/xfs/mehr.h | 77 +
libs/xfs/model.c | 1157 ++
libs/xfs/ncon.c | 525 +
libs/xfs/ncon.h | 98 +
libs/xfs/node.c | 616 +
libs/xfs/owp.c | 375 +
libs/xfs/owp.h | 86 +
libs/xfs/path.c | 1503 ++
libs/xfs/perm.c | 805 +
libs/xfs/platform.h | 51 +
libs/xfs/readme.c | 193 +
libs/xfs/schwarzschraube.c | 334 +
libs/xfs/schwarzschraube.h | 118 +
libs/xfs/simcon.c | 214 +
libs/xfs/spen.c | 963 +
libs/xfs/spen.h | 121 +
libs/xfs/tar.c | 1225 ++
libs/xfs/teleport.c | 460 +
libs/xfs/teleport.h | 108 +
libs/xfs/tree.c | 717 +
libs/xfs/unix/operations.c | 2150 ++
libs/xfs/unix/operations.h | 54 +
libs/xfs/unix/platform.c | 359 +
libs/xfs/unix/security.c | 24 +
libs/xfs/win/operations.c | 2666 +++
libs/xfs/win/operations.h | 50 +
libs/xfs/win/platform.c | 541 +
libs/xfs/win/security.c | 1935 ++
libs/xfs/xencro.c | 944 +
libs/xfs/xencro.h | 118 +
libs/xfs/xencws.c | 5090 +++++
libs/xfs/xencws.h | 71 +
libs/xfs/xfs-priv.h | 118 +
libs/xfs/xfs.c | 403 +
libs/xfs/xgap.c | 1408 ++
libs/xfs/xgap.h | 244 +
libs/xfs/xgapf.c | 1822 ++
libs/xfs/xgapf.h | 126 +
libs/xfs/xgapk.c | 1777 ++
libs/xfs/xgapk.h | 184 +
libs/xfs/xhttp.c | 2998 +++
libs/xfs/xhttp.h | 174 +
libs/xfs/xlog.c | 295 +
libs/xfs/xtar.c | 1248 ++
libs/xfs/xtar.h | 160 +
libs/xfs/zehr.c | 1063 +
libs/xfs/zehr.h | 266 +
local-builds.sh | 72 +
schema_crc.pl | 148 +
setup/install.prl | 43 +-
setup/konfigure.perl | 160 +-
setup/package.prl | 63 +-
test/Makefile | 41 +-
test/align-cache/CSRA_file | Bin 154937 -> 0 bytes
test/align-cache/Makefile | 58 -
test/align-cache/valgrind.suppress | 6 -
test/align-info/Makefile | 48 -
test/cc/Makefile | 60 +
test/cc/asm-test.cpp | 465 +
test/cipher/Makefile | 52 +
test/cipher/test.sh | 47 +
test/copycat/Makefile | 60 -
test/copycat/input/1.xml | 5 -
test/ext/Makefile | 51 +
test/ext/magic/Makefile | 61 +
test/ext/magic/magictest.cpp | 85 +
test/fastq-loader/.gitignore | 1 -
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test/fastq-loader/expected/1.1.stdout | 32 -
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test/fastq-loader/expected/2.8.1.stdout | 64 -
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test/fastq-loader/expected/3.1.stdout | 128 -
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test/fastq-loader/expected/4.5.1.stderr | 8 -
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test/fastq-loader/test-fastq-loader.cpp | 215 -
test/fastq-loader/wb-test-fastq.cpp | 1396 --
test/general-loader/.gitignore | 2 -
test/general-loader/Makefile | 183 -
test/general-loader/expected/1.stdout | 75 -
test/general-loader/expected/1override.stdout | 75 -
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test/general-loader/makeinputs.cpp | 226 -
test/general-loader/runtestcase.sh | 108 -
test/general-loader/schema/.gitignore | 4 -
test/general-loader/test-general-loader.cpp | 1684 --
test/general-loader/test-general-writer.cpp | 341 -
test/general-loader/test-gw-dumper.cpp | 80 -
test/general-loader/testsource.cpp | 758 -
test/general-loader/testsource.hpp | 177 -
test/judy_test/Makefile | 58 +
test/judy_test/judytest.c | 1831 ++
test/junit-4.11.jar | Bin 0 -> 288666 bytes
test/kapp/Makefile | 169 +
test/kapp/env-test-tool.c | 170 +
test/kapp/kapp-test.cpp | 549 +
test/kapp/qfiletest.c | 338 +
test/kapp/queuefile.data | 338 +
test/kapp/report-kns-agent.c | 58 +
test/kapp/run-kns-agent.sh | 60 +
test/kapp/run-sig-core.sh | 116 +
test/kapp/sig-core.c | 101 +
test/kar/Makefile | 55 -
test/kar/expected/1.0.stdout | 35 -
test/kar/input/1.0/sub1/col/sub1/idx2 | 0
test/kar/input/1.0/sub1/col/sub1/idx3 | 0
test/kar/input/1.0/sub1/md/cur | 0
test/kar/input/1.0/sub1/sub2/col/sub1/idx | 0
test/kar/input/1.0/sub1/sub2/col/sub1/idx0 | 0
test/kar/input/1.0/sub1/sub2/col/sub1/idx1 | 0
test/kar/input/1.0/sub1/sub2/col/sub1/idx2 | 0
test/kar/input/1.0/sub1/sub2/col/sub1/idx3 | 0
test/kar/test-kar.sh | 97 -
test/kdb/Makefile | 103 +
test/kdb/kdbtest.cpp | 174 +
test/kdb/remote_open_test.cpp | 304 +
test/kdb/root/sra/SRR000123.sra.cache | Bin 0 -> 2975732 bytes
test/kdb/test-btree.c | 338 +
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test/kdb/wkdbtest.cpp | 264 +
test/kfc/Makefile | 57 +
test/kfc/kfc.c | 29 +
test/kfc/test-except.c | 133 +
test/kfg/Makefile | 139 +
test/kfg/config.linux.kfg | 26 +
test/kfg/config.schema.kfg | 25 +
test/kfg/config.sra.kfg | 29 +
test/kfg/flat-sra-kfg.cpp | 415 +
test/kfg/flat-sra-kfg/aux_root/empty.kfg | 1 +
test/kfg/flat-sra-kfg/new/sraFlat.kfg | 1 +
test/kfg/flat-sra-kfg/old/fuse1000.kfg | 1 +
test/kfg/keystoretest.cpp | 429 +
test/kfg/kfgtest.cpp | 1030 +
test/kfg/ncbi-home-from-env.configs/dir1/file.kfg | 2 +
.../dir1/not-user-settings.xml | 2 +
.../dir1/user-settings.mkfg | 2 +
test/kfg/ncbi-home-from-env.configs/dir2/file.kfg | 2 +
.../dir2/not-user-settings.xml | 2 +
.../dir2/user-settings.mkfg | 2 +
test/kfg/ncbi-home-from-env.cpp | 50 +
test/kfg/prj_2956.ngc | Bin 0 -> 91 bytes
test/kfg/repositorytest.cpp | 280 +
test/kfg/wb-test-kfg.cpp | 628 +
test/kfs/Makefile | 137 +
test/kfs/cacheteetest.cpp | 604 +
test/kfs/kfstest.cpp | 198 +
test/kfs/md5test.cpp | 199 +
test/kfs/ramfiletest.cpp | 199 +
test/kfs/resolvetest.cpp | 196 +
test/kfs/test.tar | Bin 0 -> 20480 bytes
test/kget/.gitignore | 3 -
test/kget/Makefile | 66 -
test/kget/test_kget.py | 175 -
test/klib/Makefile | 198 +
test/klib/asm-test.c | 114 +
test/klib/md5appendtest.c | 274 +
test/klib/printf-test.c | 836 +
test/klib/test-SraReleaseVersion.cpp | 316 +
test/klib/test-klib.cpp | 1027 +
test/klib/test-log.cpp | 317 +
test/klib/test-out.cpp | 156 +
test/klib/test-vnamelist.cpp | 364 +
test/kns/KNSManagerSingletonTest.cpp | 69 +
test/kns/Makefile | 122 +
test/kns/http-test.c | 368 +
test/kns/http_dropconnection_test.cpp | 437 +
test/kns/httptest.cpp | 870 +
test/kns/knstest.cpp | 1074 +
test/kns/nih_1_out.txt | 277 +
test/kproc/Makefile | 55 +
test/kproc/kproctest.cpp | 889 +
test/krypto/Makefile | 215 +
test/krypto/test-aes-ciphers.c | 792 +
test/krypto/test-cipher-speed.c | 910 +
test/krypto/test-cmn.cpp | 359 +
test/krypto/test-cmn.hpp | 90 +
test/krypto/test-csprng.c | 230 +
test/krypto/test-encdec.cpp | 607 +
test/krypto/test-krypto-slow.cpp | 401 +
test/krypto/test-modes.c | 1261 ++
test/krypto/test-reenc.cpp | 376 +
test/ktst/Makefile | 60 +
test/ktst/ktsttest.cpp | 186 +
test/loader/Makefile | 58 +
test/loader/loadertest.cpp | 407 +
test/loader/sequence-writer.c | 366 +
test/loader/sequencewriter.vschema | 47 +
test/network-test/Makefile | 99 -
test/network-test/network-test.c | 105 -
test/network-test/network-test.vers | 1 -
test/network-test/network-testing.c | 436 -
test/network-test/network-testing.h | 42 -
test/ngs-c++/CSRA1PileupTest.cpp | 742 +
test/ngs-c++/CSRA1_ReadCollection_test.cpp | 252 +
test/ngs-c++/CSRA1test.cpp | 1116 +
test/ngs-c++/Makefile | 127 +
test/ngs-c++/NGStest.cpp | 71 +
test/ngs-c++/SRADBtest.cpp | 536 +
test/ngs-c++/SRAtest.cpp | 478 +
test/ngs-c++/SRR600096 | Bin 0 -> 81253 bytes
test/ngs-c++/SRR611340 | Bin 0 -> 211261 bytes
test/ngs-c++/ngsfixture.hpp | 93 +
test/ngs-c++/seq_spot_id_0.sra | Bin 0 -> 14316329 bytes
test/ngs-c++/valgrind.suppress | 12 +
test/ngs-java/Makefile | 125 +
test/ngs-java/build.xml | 53 +
test/ngs-java/ngs_test_CSRA1.java | 860 +
test/ngs-java/ngs_test_lib_load.java | 246 +
test/ngs-pileup/Makefile | 137 -
test/ngs-pileup/runtestcase.sh | 90 -
test/ngs-pileup/test-ngs-pileup.cpp | 177 -
test/ngs-python/Makefile | 57 +
test/ngs-python/build.xml | 41 +
test/ngs-python/tests.py | 506 +
test/ngs/Makefile | 216 +
test/ngs/data/.gitignore | 1 +
test/ngs/data/SysPathTest/md/cur | Bin 0 -> 21398 bytes
test/ngs/data/SysPathTest/md5 | 1 +
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.../data/SysPathTest/tbl/SEQUENCE/col/READ}/idx0 | 0
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test/ngs/data/SysPathTest/tbl/SEQUENCE/md5 | 1 +
test/ngs/ngs_c_fixture.hpp | 180 +
test/ngs/ngstest.cpp | 889 +
test/ngs/ngstest_csra1.cpp | 1250 ++
test/ngs/ngstest_csra1_pileup.cpp | 577 +
test/ngs/ngstest_csra1_readcollection.cpp | 739 +
test/ngs/ngstest_csra1_refwin.cpp | 819 +
test/ngs/ngstest_fragmentblob.cpp | 597 +
test/ngs/ngstest_makedb.cpp | 196 +
test/ngs/ngstest_reference.cpp | 133 +
test/ngs/ngstest_sra.cpp | 1065 +
test/ngs/ngstest_sradb.cpp | 866 +
test/ngs/valgrind.suppress | 16 +
test/pileup-stats/Makefile | 61 -
test/pileup-stats/valgrind.suppress | 6 -
test/ref-variation/Makefile | 62 -
test/ref-variation/expected/ref-variation.out | 192 -
test/ref-variation/expected/var-expand.out | 1 -
test/ref-variation/have-access.sh | 25 -
test/ref-variation/ref-variation.in | 4 -
test/ref-variation/ref-variation.sh | 29 -
test/samline/Makefile | 115 -
test/samline/alig-gen.c | 656 -
test/samline/bx_tag_test.py | 27 -
test/samline/ca_test.py | 80 -
test/samline/cigar.c | 446 -
test/samline/cigar.h | 59 -
test/samline/example.sh | 61 -
test/samline/refbases.c | 184 -
test/samline/refbases.h | 43 -
test/samline/reject_multi_refnames.sh | 62 -
test/samline/sam.py | 339 -
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test/search/Makefile | 61 +
test/search/PerfCounter.h | 211 +
test/search/agrep-main.c | 346 +
test/search/search-vdb.cpp | 512 +
test/search/search-vdb.h | 229 +
test/search/test-agrep.cpp | 928 +
test/sraxf/Makefile | 60 +
test/sraxf/fix_read_seg-test.cpp | 131 +
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vdb3/src/kfc/log.cpp | 142 +
vdb3/src/kfc/memmgr.cpp | 162 +
vdb3/src/kfc/memory.cpp | 392 +
vdb3/src/kfc/pfdmgr.cpp | 64 +
vdb3/src/kfc/pfdmgr.hpp | 68 +
vdb3/src/kfc/plogger.cpp | 148 +
vdb3/src/kfc/plogger.hpp | 72 +
vdb3/src/kfc/pmemmgr.cpp | 315 +
vdb3/src/kfc/pmemmgr.hpp | 75 +
vdb3/src/kfc/ptimemgr.cpp | 81 +
vdb3/src/kfc/ptimemgr.hpp | 64 +
vdb3/src/kfc/ptr.cpp | 206 +
vdb3/src/kfc/ref.cpp | 140 +
vdb3/src/kfc/refcount.cpp | 113 +
vdb3/src/kfc/rsrc.cpp | 141 +
vdb3/src/kfc/stream.cpp | 395 +
vdb3/src/kfc/string.cpp | 1324 ++
vdb3/src/kfc/syserr.cpp | 97 +
vdb3/src/kfc/task-impl.cpp | 352 +
vdb3/src/kfc/task.cpp | 109 +
vdb3/src/kfc/time.cpp | 290 +
vdb3/src/kfc/timemgr.cpp | 105 +
vdb3/src/kfc/vers.cpp | 85 +
3316 files changed, 836787 insertions(+), 296394 deletions(-)
--
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