[med-svn] [Git][med-team/plink2][master] 5 commits: See https://lists.debian.org/debian-med/2022/08/msg00025.html

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / plink2


Commits:
0d168792 by Andreas Tille at 2022-12-12T09:23:45+01:00
See https://lists.debian.org/debian-med/2022/08/msg00025.html

- - - - -
02d8b737 by Andreas Tille at 2022-12-12T09:32:31+01:00
Fix watch file

- - - - -
358a17ba by Andreas Tille at 2022-12-12T09:33:29+01:00
New upstream version 2.00~a3.5-220809+dfsg
- - - - -
851217d2 by Andreas Tille at 2022-12-12T09:33:32+01:00
Update upstream source from tag 'upstream/2.00_a3.5-220809+dfsg'

Update to upstream version '2.00~a3.5-220809+dfsg'
with Debian dir 4a1a2ec178da65c6d8e00399937d3dcc8743cdfb
- - - - -
e1479acc by Andreas Tille at 2022-12-12T09:47:47+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/patches/baseline
- debian/watch
- include/plink2_base.h
- plink2.cc
- plink2_merge.cc


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+plink2 (2.00~a3.5-220809+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * Fix watch file (seems we are at ~a3.5 released at 220809)
+
+ -- Andreas Tille <tille at debian.org>  Mon, 12 Dec 2022 09:35:02 +0100
+
 plink2 (2.00~a3.3-220801+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/baseline
=====================================
@@ -8,7 +8,7 @@ Forwarded: not-needed
  
  # BASEFLAGS=-g -DZSTD_MULTITHREAD -DSTATIC_ZSTD
 -BASEFLAGS=-g -mavx2 -mbmi -mbmi2 -mfma -mlzcnt -DZSTD_MULTITHREAD
-+BASEFLAGS=-g -DZSTD_MULTITHREAD
++BASEFLAGS=-g -mfma -DZSTD_MULTITHREAD
  # BASEFLAGS=-g -msse4.2 -DZSTD_MULTITHREAD
  
  include Makefile.src


=====================================
debian/watch
=====================================
@@ -1,3 +1,10 @@
 version=4
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,uversionmangle=s/(\d\S+)/2.00~a3.3-$1/,repack,compression=xz" \
- https://www.cog-genomics.org/plink/2.0/ /static/bin/plink2_src_(\d\S+)\.zip
+
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,uversionmangle=s/(\d\S+)/2.00~a3.5-$1/" \
+ https://www.cog-genomics.org/plink/2.0/dev /static/bin/plink2_src_(\d\S+)\.zip
+
+# There are newer tags on github than on cog-genomics.org but this is a mixed tarball of version 1.9 and 2.0
+# The "version" ~a3.5 above was guessed from the github tags at the date encoded in the zip file name
+#opts="repacksuffix=+dfsg,dversionmangle=auto,uversionmangle=s/a/~a/,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
+#   https://github.com/chrchang/plink-ng/tags (?:.*?/)?v?@ANY_VERSION@@ARCHIVE_EXT@
+


=====================================
include/plink2_base.h
=====================================
@@ -713,7 +713,7 @@ CONSTI32(kBytesPerVec, 32);
 // However, processor power management, numeric libraries, and my AVX2 code
 // should improve over time.  There will probably come a time where switching
 // to 32-byte fp is worthwhile.
-#define FVEC_32
+// #define FVEC_32
 
 // bleah, have to define these here, vector_size doesn't see enum values
 typedef uintptr_t VecW __attribute__ ((vector_size (32)));


=====================================
plink2.cc
=====================================
@@ -44,7 +44,7 @@
 namespace plink2 {
 #endif
 
-static const char ver_str[] = "PLINK v2.00a3.4"
+static const char ver_str[] = "PLINK v2.00a3.5"
 #ifdef NOLAPACK
   "NL"
 #endif
@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a3.4"
 #ifdef USE_MKL
   " Intel"
 #endif
-  " (1 Aug 2022)";
+  " (9 Aug 2022)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   " "


=====================================
plink2_merge.cc
=====================================
@@ -5539,6 +5539,8 @@ PglErr MergePgenVariantNoTmpLocked(SamePosPvarRecord** same_id_records, const Al
       } else {
         reterr = PgrGetMDp(sample_include, cur_mrp->pssi, read_sample_ct, read_variant_uidx, pgrp, pgvp);
       }
+      // bugfix (9 Aug 2022)
+      ZeroTrailingNyps(read_sample_ct, pgvp->genovec);
       if (unlikely(reterr)) {
         PgenErrPrintNV(reterr, read_variant_uidx);
         goto MergePgenVariantNoTmpLocked_ret_1;



View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/3966fd8542ef1088dd35eed6bac3fac3943fb94c...e1479accf4cf0cd6cd67879e7d8b743b957cbe02

-- 
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/compare/3966fd8542ef1088dd35eed6bac3fac3943fb94c...e1479accf4cf0cd6cd67879e7d8b743b957cbe02
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