Andreas Tille pushed to branch master at Debian Med / libtabixpp
Commits: 7a71f0f6 by Andreas Tille at 2023-01-19T09:54:36+01:00 New upstream version 1.1.2 - - - - - ec4222b8 by Andreas Tille at 2023-01-19T09:54:36+01:00 routine-update: New upstream version - - - - - 269131ba by Andreas Tille at 2023-01-19T09:54:36+01:00 Update upstream source from tag 'upstream/1.1.2' Update to upstream version '1.1.2' with Debian dir c996b962c48053f32a48ecb4cc8ad5a862284f8a - - - - - d96ef434 by Andreas Tille at 2023-01-19T09:54:37+01:00 routine-update: Standards-Version: 4.6.2 - - - - - 31fad88a by Andreas Tille at 2023-01-19T09:54:45+01:00 Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. Changes-By: lintian-brush - - - - - cf074041 by Andreas Tille at 2023-01-19T09:55:51+01:00 routine-update: Ready to upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - debian/upstream/metadata - tabix.hpp Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +libtabixpp (1.1.2-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.6.2 (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. + + -- Andreas Tille <ti...@debian.org> Thu, 19 Jan 2023 09:54:58 +0100 + libtabixpp (1.1.1-1) unstable; urgency=medium [ Andreas Tille ] ===================================== debian/control ===================================== @@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, d-shlibs -Standards-Version: 4.6.0 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/libtabixpp Vcs-Git: https://salsa.debian.org/med-team/libtabixpp.git Homepage: https://github.com/ekg/tabixpp ===================================== debian/upstream/metadata ===================================== @@ -1,5 +1,5 @@ --- -Bug-Database: https://github.com/ekg/tabixpp/issues -Bug-Submit: https://github.com/ekg/tabixpp/issues/new +Bug-Database: https://github.com/vcflib/tabixpp/issues +Bug-Submit: https://github.com/vcflib/tabixpp/issues/new Repository: https://github.com/ekg/tabixpp.git -Repository-Browse: https://github.com/ekg/tabixpp +Repository-Browse: https://github.com/vcflib/tabixpp ===================================== tabix.hpp ===================================== @@ -1,3 +1,5 @@ +#pragma once + #include <string> #include <stdlib.h> #include <sys/stat.h> @@ -24,6 +26,30 @@ class Tabix { bool has_jumped; vector<string>::iterator current_chrom; + /* uncompressed file pos + off_t hts_utell1(htsFile *fp) + { + if (fp->is_bgzf) { + return bgzf_htell(fp->fp.bgzf); + } + else + return htell(fp->fp.hfile); + } + */ + + // Get file position in compressed file - really on disk + off_t bgzf_htell1(BGZF *fp) { + if (fp->mt) { + return -1; // skip if multithreading + //pthread_mutex_lock(&fp->mt->job_pool_m); + //off_t pos = fp->block_address + fp->block_clength; + //pthread_mutex_unlock(&fp->mt->job_pool_m); + //return pos; + } else { + return htell(fp->fp); + } +} + public: string filename; vector<string> chroms; @@ -37,5 +63,6 @@ public: bool setRegion(string& region); bool getNextLine(string& line); bool getNextLineKS(); - + // Specialised function gets actual file position when using bgzf + long file_pos() { return bgzf_htell1(fn->fp.bgzf); }; }; View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/compare/c28d16d3b0e51f76d54b0409e9659fc89d6b163f...cf0740413b2f665f910c29243604d290e671b674 -- View it on GitLab: https://salsa.debian.org/med-team/libtabixpp/-/compare/c28d16d3b0e51f76d54b0409e9659fc89d6b163f...cf0740413b2f665f910c29243604d290e671b674 You're receiving this email because of your account on salsa.debian.org.
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