[med-svn] [Git][med-team/beagle][master] 2 commits: Update upstream docs

Sat Jul 19 09:08:58 BST 2025


Dylan Aïssi pushed to branch master at Debian Med / beagle


Commits:
c3117a37 by Dylan Aïssi at 2025-07-19T10:00:58+02:00
Update upstream docs

- - - - -
88ce7726 by Dylan Aïssi at 2025-07-19T10:08:15+02:00
Update debian/copyright

- - - - -


8 changed files:

- debian/beagle-doc.doc-base
- debian/beagle-doc.install
- debian/changelog
- debian/copyright
- debian/source/include-binaries
- + debian/upstream.docs/beagle.pdf
- − debian/upstream.docs/beagle_5.1.pdf
- debian/upstream.docs/release_notes


Changes:

=====================================
debian/beagle-doc.doc-base
=====================================
@@ -3,7 +3,7 @@ Title: Beagle
 Section: Science/Biology
 
 Format: PDF
-Files: /usr/share/doc/beagle/beagle_5.1.pdf.gz
+Files: /usr/share/doc/beagle/beagle.pdf.gz
 
 Format: HTML
 Index: /usr/share/doc/beagle/api/index.html


=====================================
debian/beagle-doc.install
=====================================
@@ -1,5 +1,5 @@
 debian/tests/run-sample-analysis /usr/share/doc/beagle/examples/
 debian/upstream.docs/run.beagle.example /usr/share/doc/beagle/examples/
 debian/upstream.docs/test.vcf /usr/share/doc/beagle/examples/
-debian/upstream.docs/beagle_5.1.pdf /usr/share/doc/beagle/
+debian/upstream.docs/beagle.pdf /usr/share/doc/beagle/
 debian/_jh_build.javadoc/api /usr/share/doc/beagle


=====================================
debian/changelog
=====================================
@@ -1,6 +1,7 @@
 beagle (250227-1) UNRELEASED; urgency=medium
 
   * New upstream version 250227
+  * Update debian/copyright
 
  -- Dylan Aïssi <daissi at debian.org>  Sat, 19 Jul 2025 09:44:33 +0200
 


=====================================
debian/copyright
=====================================
@@ -6,15 +6,15 @@ Comment: Remove embedded htsjdk (samtools)
 Files-Excluded: net
 
 Files: *
-Copyright: 2013-2021 Brian L. Browning
+Copyright: 2013-2025 Brian L. Browning
 License: GPL-3+
 
 Files: debian/*
-Copyright: 2016-2021 Dylan Aïssi <daissi at debian.org>
+Copyright: 2016-2025 Dylan Aïssi <daissi at debian.org>
 License: GPL-3+
 
 Files: debian/upstream.docs/*
-Copyright: 2013-2021 Brian L. Browning
+Copyright: 2013-2025 Brian L. Browning
 License: GPL-3+
 
 License: GPL-3+
@@ -29,8 +29,7 @@ License: GPL-3+
  GNU General Public License for more details.
  .
  You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+ along with this program.  If not, see <https://www.gnu.org/licenses/>.
  .
  On Debian systems, the full text of the GNU General Public License
  version 3 can be found in `/usr/share/common-licenses/GPL-3'.


=====================================
debian/source/include-binaries
=====================================
@@ -1,2 +1,2 @@
 debian/upstream.docs/beagle_4.1_09Feb16.docx
-debian/upstream.docs/beagle_5.1.pdf
+debian/upstream.docs/beagle.pdf


=====================================
debian/upstream.docs/beagle.pdf
=====================================
Binary files /dev/null and b/debian/upstream.docs/beagle.pdf differ


=====================================
debian/upstream.docs/beagle_5.1.pdf deleted
=====================================
Binary files a/debian/upstream.docs/beagle_5.1.pdf and /dev/null differ


=====================================
debian/upstream.docs/release_notes
=====================================
@@ -135,3 +135,65 @@ Beagle 5.2 (29May21.d6d) release notes
 Beagle 5.2 (28Jun21.220) release notes
 ============================================
 * Improve robustness when many markers have a high rate of missing genotypes
+
+Beagle 5.3 (08Feb22.fa4) release notes
+============================================
+* Initial release of Beagle 5.3
+* Version 5.3 has improved parameter estimation when analyzing non-human data
+* Version 5.3 has an "em" parameter that can turn off parameter estimation.
+
+Beagle 5.4 (19Mar22.0da) release notes
+============================================
+* Initial release of Beagle 5.4
+* Version 5.4 is more robust to poorly-estimated genetic maps
+* Version 5.4 has modestly lower memory requirements
+
+Beagle 5.4 (25Mar22.4f6) release notes
+============================================
+* Fix a logic bug.
+
+Beagle 5.4 (12Apr22.32e) release notes
+============================================
+* Allow break-end replacement strings in ALT alleles
+
+Beagle 5.4 (18Apr22.4de) release notes
+============================================
+* Improve error messages
+* Reduce memory use
+
+Beagle 5.4 (19Apr22.7c0) release notes
+============================================
+* Fix a bug that can be triggered when the ALT field is "."
+
+Beagle 5.4 (05May22.33a) release notes
+============================================
+* Fix an output-truncating bug when combining ref and chrom parameters
+
+Beagle 5.4 (22Jul22.46e) release notes
+============================================
+* Fix a bug in calculating the cumulative marker count
+
+Beagle 5.4 (01Mar24.d36) release notes
+============================================
+* Add an output VCF meta-information line for the INFO/END field
+
+Beagle 5.4 (27May24.118) release notes
+============================================
+* Fix a file decompression bug
+
+Beagle 5.4 (06Aug24.a91) release notes
+============================================
+* Restore Java 8 compatibility
+
+Beagle 5.4 (29Oct24.c8e) release notes
+============================================
+*  Improve handling of atypical input data
+
+Beagle 5.5 (beagle.17Dec24.224.jar) release notes
+============================================
+* Initial release of Beagle 5.5
+* Add window-markers parameter to control maximum markers per window
+
+Beagle 5.5 (27Feb25.75f) release notes
+============================================
+* Fix a bug that could cause a run-time exception
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/beagle/-/compare/00e17de2387030bdd5889f1140501c52d86c0db0...88ce772637edc79f8ae64017eb4d8a326bd2a521

-- 
View it on GitLab: https://salsa.debian.org/med-team/beagle/-/compare/00e17de2387030bdd5889f1140501c52d86c0db0...88ce772637edc79f8ae64017eb4d8a326bd2a521
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