[med-svn] [Git][med-team/libtabixpp][master] 6 commits: New upstream version 1.1.2

[Andreas Tille (@tille)]

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 <tille at 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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20230119/2c4b5a11/attachment-0001.htm>