[med-svn] [Git][med-team/plink1-9][master] 4 commits: New upstream version 1.90~b5.3-180221

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / plink1.9


Commits:
179bb503 by Dylan Aïssi at 2018-03-08T21:45:50+01:00
New upstream version 1.90~b5.3-180221
- - - - -
a142d833 by Dylan Aïssi at 2018-03-08T21:45:54+01:00
Merge tag 'upstream/1.90_b5.3-180221'

Upstream version 1.90~b5.3-180221

- - - - -
2dae8eb5 by Dylan Aïssi at 2018-03-08T21:55:40+01:00
Update changelogs

- - - - -
caee70d9 by Dylan Aïssi at 2018-03-08T22:01:44+01:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/upstream.docs/upstream.changelog
- plink.c
- plink_data.c


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+plink1.9 (1.90~b5.3-180221-1) unstable; urgency=medium
+
+  * New upstream release.
+
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Thu, 08 Mar 2018 21:50:36 +0100
+
 plink1.9 (1.90~b5.2-180109-1) unstable; urgency=medium
 
   * New upstream release.


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper (>= 11~),
                help2man,
                libatlas-base-dev,
                liblapack-dev,


=====================================
debian/upstream.docs/upstream.changelog
=====================================
--- a/debian/upstream.docs/upstream.changelog
+++ b/debian/upstream.docs/upstream.changelog
@@ -1,5 +1,7 @@
 # Copy/Paste from https://www.cog-genomics.org/plink/1.9/
 
+21 Feb 2018: "--indiv-sort file" no longer scrambles the phenotypes when used with --{b}merge or --merge-list.
+
 9 Jan 2018: --all-pheno no longer gets into an infinite loop when one phenotype is all-missing.
 
 20 Dec 2017: --meta-analysis 'report-all' now reports original stats instead of 'NA' when N=1. Fixed an inaccuracy in --adjust's handling of very small p-values. --make-just-fam works properly with just .fam input again.


=====================================
plink.c
=====================================
--- a/plink.c
+++ b/plink.c
@@ -93,7 +93,7 @@
 
 static const char ver_str[] =
 #ifdef STABLE_BUILD
-  "PLINK v1.90b5.2"
+  "PLINK v1.90b5.3"
 #else
   "PLINK v1.90p"
 #endif
@@ -105,10 +105,10 @@ static const char ver_str[] =
 #else
   " 32-bit"
 #endif
-  " (9 Jan 2018)";
+  " (21 Feb 2018)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
-  " "
+  ""
 #ifdef STABLE_BUILD
   " " // (don't want this when version number has two trailing digits)
 #else


=====================================
plink_data.c
=====================================
--- a/plink_data.c
+++ b/plink_data.c
@@ -16203,11 +16203,11 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam
     }
     if (is_dichot_pheno) {
       if (qsort_ext(sample_fids, tot_sample_ct, max_sample_full_len, merge_nsort? strcmp_natural_deref : strcmp_deref, pheno_c_char, 1)) {
-	goto merge_datasets_ret_NOMEM;
+        goto merge_datasets_ret_NOMEM;
       }
     } else {
       if (qsort_ext(sample_fids, tot_sample_ct, max_sample_full_len, merge_nsort? strcmp_natural_deref : strcmp_deref, (char*)pheno_d, sizeof(double))) {
-	goto merge_datasets_ret_NOMEM;
+        goto merge_datasets_ret_NOMEM;
       }
     }
     if (sample_sort == SAMPLE_SORT_FILE) {
@@ -16284,10 +16284,12 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam
 	  goto merge_datasets_ret_WRITE_FAIL;
 	}
 	if (is_dichot_pheno) {
-	  cc = pheno_c_char[ulii];
+          // bugfix (21 Feb 2018): need to use the map_reverse index here,
+          // since the phenotypes correspond to ASCII-sorted sample ID order.
+	  cc = pheno_c_char[ujj];
 	  fprintf(outfile, "\t%s\n", cc? ((cc == 1)? "2" : "-9") : "1");
 	} else {
-	  fprintf(outfile, "\t%g\n", pheno_d[ulii]);
+	  fprintf(outfile, "\t%g\n", pheno_d[ujj]);
 	}
       }
     }



View it on GitLab: https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c

---
View it on GitLab: https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/debian-med-commit/attachments/20180308/f405abae/attachment-0001.html>