htsfile-1.10.2-bp153.2.5.1<>,gLa!M@eeen̶U %f@xXޞ nj~ş\ETـ+fgm(ՄF5(,sl}/%saݽ f5 a:)_]gLm4?x$|)Uۉ8!` :h6FGы",.,1гU܈>cý[N EV b(MSj0uŁ{lnJ VMڋٳkF{QA; DP,>>6?6d   d $ P  f  |       , c  H( #8 , 9 \ : T F1G1 H1L I1x X1Y1\1 ]1 ^2Lb3c3d4Pe4Uf4Xl4Zu4p v4w5 x6 y6H z6x6666Chtsfile1.10.2bp153.2.5.1Identify high-throughput sequencing data files from the HTSlib projectHTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and the bgzip compression utility.aobs-arm-9 ߧSUSE Linux Enterprise 15openSUSEMIThttp://bugs.opensuse.orgProductivity/Scientific/Otherhttps://github.com/samtools/htslib/linuxaarch64 M  A^A큤A큤aa]HGSa\+*]HG[ ]]]HG65039748d72a2dd9852f1e219f19d110ded5447e3998418b5f5f291a5f30af0ebf903381b7833c785c5ac0e98f8793d77c0576e2ce8c6c08279dafda1a2ba0c95e55efa42792ae7ee2911333a5046d6cbff337f6544c7e161a0bba93bc225e7e0bd81023e565dfb16b9ffdefed0eea4a1884ddaa8efcb957db84f595caf8c082debc6f5c4c9928544c6fc3f9fa563c8a73bcdb6a2a5fb7a351dd6f8349353fa246502088d4efe181d0fc42cd046cb747a99d882c49e87740172bf4c7b841fc8fc242e1e997abb944668ccb957d91caa314acfc362572c79fde34391e8a38dfe5e72f1aded2b79ccbfba42747793e8a2e2480fd1531fe1989415d4f888ee29ee53561a9915ab1f7d68d5dd55ad38fc6062eaae2bf6be2423a91e8bc31d555432arootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootrootlibhts-1.10.2-bp153.2.5.1.src.rpmhtsfilehtsfile(aarch-64)@@@@@@@@@@@@    ld-linux-aarch64.so.1()(64bit)ld-linux-aarch64.so.1(GLIBC_2.17)(64bit)libbz2.so.1()(64bit)libc.so.6()(64bit)libc.so.6(GLIBC_2.17)(64bit)libcurl.so.4()(64bit)libhts3liblzma.so.5()(64bit)liblzma.so.5(XZ_5.0)(64bit)libpthread.so.0()(64bit)libpthread.so.0(GLIBC_2.17)(64bit)libz.so.1()(64bit)libz.so.1(ZLIB_1.2.0)(64bit)rpmlib(CompressedFileNames)rpmlib(FileDigests)rpmlib(PayloadFilesHavePrefix)rpmlib(PayloadIsXz)1.10.23.0.4-14.6.0-14.0-15.2-14.14.1a ^AE^:@[[GBYf@Ycl@Ycl@W$@W$@WWPierre Bonamy Todd R Todd R flyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.orgflyos@mailoo.org- CVE-2020-36403.diff: Add patch fixing CVE-2020-36403 #boo1187917- Include baselibs.conf as source file. - Update baselibs.conf.- Update to release 1.10.2 * This is a release fix that corrects minor inconsistencies discovered in previous deliverables. - Update to release 1.10.1 * The support for 64-bit coordinates in VCF brought problems for files not conforming to VCF/BCF specification. While previous versions would make out-of-range values silently overflow creating nonsense values but parseable file, the version 1.10 would silently create an invalid BCF. - Update to release 1.10 + Brief summary * Addition of support for references longer than 2Gb (NB: SAM and VCF formats only, not their binary counterparts). This may need changes in code using HTSlib. See README.large_positions.md for more information. * Added a SAM header API. * Major speed up to SAM reading and writing. This also now supports multi-threading. * We can now auto-index on-the-fly while writing a file. This also includes to bgzipped SAM.gz. * Overhaul of the S3 interface, which now supports version 4 signatures. This also makes writing to S3 work.- Update to 1.9 * If `./configure` fails, `make` will stop working until either configure is re-run successfully, or `make distclean` is used. This makes configuration failures more obvious. (#711, thanks to John Marshall) * The default SAM version has been changed to 1.6. This is in line with the latest version specification and indicates that HTSlib supports the CG tag used to store long CIGAR data in BAM format. * bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner) * Faidx can now index fastq files as well as fasta. The fastq index adds an extra column to the `.fai` index which gives the offset to the quality values. New interfaces have been added to `htslib/faidx.h` to read the fastq index and retrieve the quality values. It is possible to open a fastq index as if fasta (only sequences will be returned), but not the other way round. (#701) * New API interfaces to add or update integer, float and array aux tags. (#694) * Add `level=` option to `hts_set_opt()` to allow the compression level to be set. Setting `level=0` enables uncompressed output. (#715) * Improved bgzip error reporting. * Better error reporting when CRAM reference files can't be opened. (#706) * Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences. (#716) * Efficiency improvements: - Small speed-up for CRAM indexing. - Reduce the number of unnecessary wake-ups in the thread pool. (#703) - Avoid some memory copies when writing data, notably for uncompressed BGZF output. (#703) * Bug fixes: - Fix multi-region iterator bugs on CRAM files. (#684) - Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files. (#687) - Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691, reported by @freeseek) - Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when removing samples. (#692, reported by @freeseek) - Fixed bug where the VCF record ref length was calculated incorrectly if an INFO END tag was present. (71b00a) - Fixed warnings found when compiling with gcc 8.1.0. (#700) - sam_hdr_read() and sam_hdr_write() will now return an error code if passed a NULL file pointer, instead of crashing. - Fixed possible negative array look-up in sam_parse1() that somehow escaped previous fuzz testing. (#731, reported by @fCorleone) - Fixed bug where cram range queries could incorrectly report an error when using multiple threads. (#734, reported by Brent Pedersen) - Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files. (#739, reported by @carsonhh)- Better formatting of the descriptions - Spec file cleaned up using spec-cleaner - Update to 1.8 * The URL to get sequences from the EBI reference server has been changed to https://. This is because the EBI no longer serve sequences via plain HTTP - requests to the http:// endpoint just get redirected. HTSlib needs to be linked against libcurl to download https:// URLs, so CRAM users who want to get references from the EBI will need to run configure and ensure libcurl support is enabled using the - -enable-libcurl option. * Added libdeflate as a build option for alternative faster compression and decompression. Results vary by CPU but compression should be twice as fast and decompression faster. * It is now possible to set the compression level in bgzip. (#675; thanks to Nathan Weeks). * bgzip now gets its own manual page. * CRAM encoding now stored MD and NM tags verbatim where the reference contains 'N' characters, to work around ambiguities in the SAM specification (samtools #717/762). Also added "store_md" and "store_nm" cram-options for forcing these tags to be stored at all locations. This is best when combined with a subsequent decode_md=0 option while reading CRAM. * Multiple CRAM bug fixes, including a fix to free and the subsequent reuse of references with `-T ref.fa`. (#654; reported by Chris Saunders) * CRAM multi-threading bugs fixed: don't try to call flush on reading; processing of multiple range queries; problems with multi-slice containers. * Fixed crashes caused when decoding some cramtools produced CRAM files. * Fixed a couple of minor rANS issues with handling invalid data. * Fixed bug where probaln_glocal() tried to allocate far more memory than needed when the query sequence was much longer than the reference. This caused crashes in samtools and bcftools mpileup when used on data with very long reads. (#572, problem reported by Felix Bemm via minimap2). * sam_prop_realn() now returns -1 (the same value as for unmapped reads) on reads that do not include at least one 'M', 'X' or '=' CIGAR operator, and no longer adds BQ or ZQ tags. BAQ adjustments are only made to bases covered by these operators so there is no point in trying to align reads that do not have them. (#572) * BAM: HTSlib now supports BAMs which include CIGARs with more than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8). * BCF/VCF: - Removed the need for long double in pileup calculations. - Sped up the synced reader in some situations. - Bug fixing: removed memory leak in bcf_copy. * CRAM: - Added support for HTS_IDX_START in cram iterators. - Easier to build when lzma header files are absent. - Bug fixing: a region query with REQUIRED_FIELDS option to disable sequence retrieval now gives correct results. - Bug fixing: stop queries to regions starting after the last read on a chromosome from incorrectly reporting errors (#651, #653; reported by Imran Haque and @egafni via pysam). * Multi-region iterator: The new structure takes a list of regions and iterates over all, deduplicating reads in the process, and producing a full list of file offset intervals. This is usually much faster than repeatedly using the old single-region iterator on a series of regions. * Curl improvements: - Add Bearer token support via HTS_AUTH_LOCATION env (#600). - Use CURL_CA_BUNDLE environment variable to override the CA (#622; thanks to Garret Kelly & David Alexander). - Speed up (removal of excessive waiting) for both http(s) and ftp. - Avoid repeatedly reconnecting by removal of unnecessary seeks. - Bug fixing: double free when libcurl_open fails. * BGZF block caching, if enabled, now performs far better (#629; reported by Ram Yalamanchili). * Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas Hickman). * Tidied up the drand48 support (intended for systems that do not provide this function). * Fixed bug where iterators on CRAM files did not propagate error return values to the caller correctly. Thanks go to Chris Saunders. * Overhauled Windows builds. Building with msys2/mingw64 now works correctly and passes all tests. * More improvements to logging output (thanks again to Anders Kaplan). * Return codes from sam_read1() when reading cram have been made consistent with those returned when reading sam/bam. Thanks to Chris Saunders (#575). * BGZF CRC32 checksums are now always verified. * It's now possible to set nthreads = 1 for cram files. * hfile_libcurl has been modified to make it thread-safe. It's also better at handling web servers that do not honour byte range requests when attempting to seek - it now sets errno to ESPIPE and keeps the existing connection open so callers can revert to streaming mode it they want to. * hfile_s3 now recalculates access tokens if they have become stale. This fixes a reported problem where authentication failed after a file had been in use for more than 15 minutes. * Fixed bug where remote index fetches would fail to notice errors when writing files. * bam_read1() now checks that the query sequence length derived from the CIGAR alignment matches the sequence length in the BAM record.- Separated the binaries from the shared lib package- Cleaner structure of the spec file and baselibs.conf, thanks to the amazing help of the packaging mailing list guys!- Update to 1.5 - Change in SONAME, updated the package name to libhts2 - New dependencies to libbz2 and lzma- Update to 1.3.1- Cleaner spec file - Added baselibs.conf- Changed "./configure" and "make install" for "%configure" and "%make_install" - Moved "%_libdir/libhts.so" and "%_libdir/pkgconfig/htslib.pc" to the *-devel package.- Initial release.obs-arm-9 1629126887 1.10.2-bp153.2.5.11.10.2-bp153.2.5.1htsfilehtsfileNEWSREADMEhtsfileLICENSEhtsfile.1.gzfaidx.5.gzsam.5.gzvcf.5.gzhtslib-s3-plugin.7.gz/usr/bin//usr/share/doc/packages//usr/share/doc/packages/htsfile//usr/share/licenses//usr/share/licenses/htsfile//usr/share/man/man1//usr/share/man/man5//usr/share/man/man7/-fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -gobs://build.opensuse.org/openSUSE:Maintenance:16823/openSUSE_Backports_SLE-15-SP3_Update/0429a4e037a94dc5977814d7649bc723-libhts.openSUSE_Backports_SLE-15-SP3_Updatedrpmxz5aarch64-suse-linuxELF 64-bit LSB shared object, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, BuildID[sha1]=a9e4039eb84584196688cf9000da4a67183373e4, for GNU/Linux 3.7.0, strippeddirectoryUTF-8 Unicode textASCII texttroff or preprocessor input, ASCII text (gzip compressed data, max compression, from Unix) R RRR RRRR RR RR=Q" 5#utf-84eaad7cf89a408925705ca72012b4d26f6927809648287154cdf3b033a2dd579? 7zXZ !t/Cp,]"k%rגbM6һ2 e*BǛAG(q~=v#'jxFu as49P#^/˟&?s_}"\{|/>.,㩸@ɶѵQ㨙悚&=ftE­ Xyc֔n:]}8\*skEr׼pm'cċ5BPOvW'ݨ oŕ¼cFR®IݸH1Inp RgX`ɝ~!UDq52BXL}zodK8M"A \MLT p6'JI р.* Q; Gr]a^Z/ԗcV>i$^6ɴ„E7zJ_g~k9~*@;o._M0O<ڙY]1qwS$NO;yYL*AG9y,F Ƃ.FGY\"*"Y*CփXeB;B}ʫ%0QGMi%ۡO*(f&^*jkoӕ#cH\2@Pd3Uz{UZtUFmI72y[nWR9+,J<191HL1Fn&sh6\ ݅ q.i@risO3Q /_ NS058)'"e:;A _.9rDD9 ڋ#o yAh_)j"a8r=⨋k E d+/K!LpgN _ /%ŅeNXnb$x\-] /.x~Uwޭ<W]R1=3DhUv$IPq|e95TYA2.W&nA@ˮTkA+W@,/EP1g6d@yУ+̓^ ΔU?ӭKρZj7I Q̑r&|kW \5J'~\$ ,ɍؙh%L29֬Ƅ|5U;ފO ɵ1U0l刂k8C\U76ٵ"[G ^(25^1C$\YBfa"ܹmڶ{tL꼥IYƫjoI_T0]őy >+_bjB%:|6[C/N8.u_Np|Ci}RB'jwInug{9^/, ˥ؒ4E99 >^ՍWxz- ȷ2j_Q )(h "&E`ALSdTU)L$o癕1tAB\ہ(o)v" TZΪs~5q.5C"&EN%9 i1nI޲$H7 ^&|^,9џk/neB=ULMXZG g5 p QYi{OR**6K&3Pn3!& Z遰rCǚ1 z@s7mTN0IҧeP kXaُ[d[MlR!̮4`q1-9]"Ќu4|7ށ:).?;1q^EGl`'mVYL)#翁f8ճ0[$(NΥd94養{d<,M݁M?qR Ktl7>IK9!ԗM8ѩ CK>b 6A^^3š ֆT[E[;Jh 'Bƚ=:/w1Lm2AI7I R){Qp!Rv* \}Hdtnc95L})vq)c> lrw_R^9Jg{))tu MwWVSfJOf<$"䯦 OKn*2Pi5t|xc?XM$a$5HI-$e@xSʵB N!r0C#/EŹ7DQHzN@r&D?ޮ:$}:C%]1Sɧ5w&~(NɄ#(ǭk6^RpMI&C:XzK@.ߩ!W  N/zγ"blhDq,FSV+l8VBg(?NjYS@*ĂM{ƨw[uo#@λ}b-]q59 i3Jrn$Wfke8l(-m û:k2l]AudX~4dFICJȗTzl$l%:2uɝ1ˑ)42[CdrF^p"C<I\D=fAD|8MZ{FIhbboa cϙynY W_&.z(GQSY('Rv_@p~4֣ߤk(\{GM"w;] u|]3HRQ1b)su~w_dYJ`T+Fg! nqs Z(@;SSY6ߒ򾅦]@+SuqbF3aY]k9rQ4>N;`'%58Hҍ}0I SeuyL JH(aĕ7Bk9-Zޝf%;hó@[̹mΔWP/Bd_*3r,? :.zlIyuwX'ruxvO]qaU[lR ;-RB)"4]S>yh̔G-n ;B" dS[< .4FjjQMi櫥̅?p"S\skͻiQVګw1 H%uZ+I~Kϡ墇#q] k~u̱Hɽg2d 7gKKkEϠIZ҆ uIկ͊dPYv r,qOuͬmN 5+ MFC7@uTLF\Rl-##=+X[(UR+3&!HP(j湊3 Rc$7 fg -* xm4םّr&0cGMfNBlj9pBEPז}jh }5@ծv+ϰ/V׸p9t#7y e9qtdaP! 0΁\~z3V=W:Wd!56HTcY֌ c- [|NKtl_${5*W}z>njب\p`aT68vvENȂGˏr0i|"4QHKxBſsLzbkS# M{Ș|[@YCPC0lܹ~] n{a224)^mgxu@e}U4;X4\lܲ*´s'8+Kk^LGG9\Z4(O9&.zD}4"xѴ$5rO2Gም./ NWy o8507JA`^5kF-AEw|:GD֩}vUg}6FZ @HdAwn[&[Vz2ySy)eN41;&;B4H<LDSN b@)L{zXצj/zERiV L;BA3+ʴd >vݥ3T! E5N"ihZT S}(y.erEs :%-_vtD~Jܦ<㲖j`W+߽HhAe4:v O7fBm0XhH@t~^oWNYf&ߗC{X^)LsF5~)A۾L_'~,gR=<n˷i""6sĂ]:ҏ)G):Ydom}+|pa`aCGDgr"^.x KJxV&4D2c2ntMdƿTz$ Y |: F޻m'sN/jӦָń?f{R\ ߆b~vJ(6a||>A%_J3o?.RJN#]4D8c"6b{e}1b|&x,X5`i|-cʽVQ3!4zbmꬨs讣{^-uݗܲMK>A_KOJ*&z,# P9} ߻wȩ60 En\ ,.2;4h:yЙZB#rc^蠸卵GhIv| f } 0uߨ3#FʹN=Ԑ Ha8JQ=aGؙ\1&qMhz2PL3@c۔A6**9:z6,xDg!+%QDɮUtpBII*9% A˾wGP.)$at 4KS#$$-d,$C'-Tlే/j~y =%ҡki7;w9wlkX1o%“#z,%:j/8f{]S?b@qrRQ%Pk袐Bc0J.ӿ!AM'h"ņpD9PD+ל ^*WCEB>QB:fB-HVO9op35UhPqK Y'ݸ_ab!~ਢ+$%"!Lz[Zr]^ }Pd/q0a FQQcԒ±=61{D1n?@:bkUҠ-+ l>nBYxkfUJZiޛ n ueK4ѡP>٨{C1|MUw _IW-^fp=.@,Ȯ.Y9_;;z$*u>>cHyPBfF47<}d%ؙAP< }Mg s 1>QS*_DdZ6?!Iߨ9lt0ϚI؈穖)Rn'ցϤVBQVy޾t4{W }]$IwaSw{97?!TSD)GW:_%(Qu|O*$ϸqͮtwRu"7_@}rvTU-wq$aM!L Ƽ,~ϓb\-DR.Dz#j'![N4s+7;$]x!&*#A߁8Y"Qle ؐQҊjNz#,rv!w?_VR%} Onpwg3>*{볥tRYJUC>'+o"廒xP{20p`|+27R;,_Ww/k*|TqZ73䪪RW?iZ+\Sb=vV/[SJqHS EQ}͒d7f?ѳbGCT}t>\gtS,^k;S$sid̬xKǖٹaӅ?e_/c8FoN Өsގ*zt)'0.CJq=Ժ5:N C@QC$脾IapCqMЏO!Y ?&HWUR&Ew76αKA:2WBhvi0ؚ]A]lf~UОnqi"6Tq‰9DfUMb.0+w%YsKa!f(: WupޖxZ/ &U"r7߂9DenU͹AeOZ0۸ok=74j*atҟ 0ʊ&O,iEm}  )㛅Qqcl0*0=glu YᣟgBK[Hjɢv}Mj'I9!W|Cl&N(u C-Iǻ#eUŢ׼n*B§@҉ҍ;/yHriyVkveS{vy?Q*DQC@zVӾF BlշNO .E ̌2۬UaO%pEz$je`^HVkMϱeCkgEsgKd:1B7{y[ιREY> M PP/q򶐹x@R2/)ku3/Zi6uAoaH"b MBBB}Wiޔeح'yF"}f ON"%8`SB^Rld_"w#l6c!}nd'$Z0F}0!Fmzp \/hʲ\]]y [RJ'ANf~eg*$D× Pt+fQHVd`lF-t<*R \X`u޵!O,ݴQgQZ j;1=ʽկ,0?8rECs9a:iCoiEK^2w֤r" !c0XSizߊ0Lv;!~;sgo%@ig(9=&O6sN N{G@%UeG%{{n&0q-Z.NXxzdhZѩŇɮ ً5 2ƦMLeCOBq @1͌ԥοIOeapRx7AxGW3bXē wʹt#ԣ:Te%VR4: rGR SwnpvDTUE*e$@ևRvE>;&`! , _ځʙCoiµ4ap~mK҇7yҳ<:"K]ȲTnV2 ū'b\VGe QG߯rZFEGSEA T@&Zx߇B/(:A4URtdZAt9Z(t-\!.4ox)y 'ZQ Q:R;dXӵXi5wRVN m<NX" YZ