[med-svn] [Git][med-team/seaview][debian/jessie-backports] 4 commits: Enable reading number of bootstraps from phyml runs

[Andreas Tille]

Andreas Tille pushed to branch debian/jessie-backports at Debian Med / seaview


Commits:
8880102e by Andreas Tille at 2017-02-01T10:14:51+01:00
Enable reading number of bootstraps from phyml runs

- - - - -
ae372fca by Andreas Tille at 2017-02-01T12:55:15+01:00
Close bug and upload

- - - - -
ecdea44d by Andreas Tille at 2017-02-06T09:44:32+01:00
Merge branch 'master' into debian/jessie-backports

- - - - -
f8a5720b by Andreas Tille at 2017-02-06T09:44:48+01:00
Rebuild for jessie-backports

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/evaluate_phyml_bootstrap_number.patch
- + debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,16 @@
+seaview (1:4.6.1.2-2~bpo8+1) jessie-backports; urgency=medium
+
+  * Rebuild for jessie-backports.
+
+ -- Andreas Tille <tille at debian.org>  Mon, 06 Feb 2017 09:44:39 +0100
+
+seaview (1:4.6.1.2-2) unstable; urgency=medium
+
+  * Enable reading number of bootstraps from phyml runs
+    Closes: #853835
+
+ -- Andreas Tille <tille at debian.org>  Wed, 01 Feb 2017 12:54:56 +0100
+
 seaview (1:4.6.1.2-1~bpo8+1) jessie-backports; urgency=medium
 
   * Rebuild for jessie-backports to become compatible with backported phyml


=====================================
debian/patches/evaluate_phyml_bootstrap_number.patch
=====================================
--- /dev/null
+++ b/debian/patches/evaluate_phyml_bootstrap_number.patch
@@ -0,0 +1,32 @@
+Description: Enable reading number of bootstraps from phyml runs
+Author: Manolo Gouy <manolo.gouy at univ-lyon1.fr>
+        Patch extracted from Upstream version 4.6.1.3
+Last-Update: Wed, 01 Feb 2017 08:51:09 +0100
+
+--- a/trees.cxx
++++ b/trees.cxx
+@@ -1201,6 +1201,24 @@ void run_phyml_callback(Fl_Widget *ob, v
+ 	  display_tree = put_names_back_in_tree(display_tree, truenames);
+     //process bootstrap trees
+     char *bootstrap_trees = NULL;
++    if (replicates > 0) {
++      sprintf(input, "%s.phy_phyml_boot_stats.txt", base_fname);
++      in = fopen(input, "r");
++      if (!in) {
++        sprintf(input, "%s.phy_phyml_boot_stats", base_fname);
++        in = fopen(input, "r");
++      }
++      if (in) { // compute the true # of bootstrap replicates because parallelized phyML can compute a few more
++        char line[150];
++        while ((p = fgets(line, sizeof(line), in))) {
++          while (*p == ' ') p++;
++          if (*p == '#') {
++            sscanf(p+1, "%d", &replicates);
++          }
++        }
++        fclose(in);
++      }
++    }
+     if (replicates > 0 && b_keep_trees->value()) {
+       sprintf(input, "%s.phy_phyml_boot_trees.txt", base_fname);
+       in = fopen(input, "r");


=====================================
debian/patches/series
=====================================
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+evaluate_phyml_bootstrap_number.patch



View it on GitLab: https://salsa.debian.org/med-team/seaview/compare/9ecce4bc02051ab0d2c82f97a18c05f11f3c276a...f8a5720bd5a0d4aa8bfe150c539a14ad412e215e

---
View it on GitLab: https://salsa.debian.org/med-team/seaview/compare/9ecce4bc02051ab0d2c82f97a18c05f11f3c276a...f8a5720bd5a0d4aa8bfe150c539a14ad412e215e
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