[med-svn] [salmon] 04/04: re-org patches

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a commit to branch master
in repository salmon.

commit 71b520eb2ed0bb79f8a9adeaa8d902f54060865c
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Jan 30 00:11:03 2016 -0800

    re-org patches
---
 debian/patches/cmake-typo-fixes | 13 +++++++++++++
 debian/patches/series           |  1 -
 debian/patches/spelling-fixes   | 11 -----------
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/debian/patches/cmake-typo-fixes b/debian/patches/cmake-typo-fixes
index f63204f..67c9795 100644
--- a/debian/patches/cmake-typo-fixes
+++ b/debian/patches/cmake-typo-fixes
@@ -1,3 +1,5 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: fix upstream's typos
 --- salmon.orig/CMakeLists.txt
 +++ salmon/CMakeLists.txt
 @@ -6,8 +6,8 @@
@@ -42,3 +44,14 @@
  //            print_help();
              return false;
          }
+--- salmon.orig/src/SalmonQuantify.cpp
++++ salmon/src/SalmonQuantify.cpp
+@@ -2928,7 +2928,7 @@
+                                         "many reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should "
+                                         "not be too large if you wish to keep a low memory usage, but setting it large enough can substantially speed up "
+                                         "inference on \"small\" files that contain only a few million reads.")
+-    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occuring more than this many times won't be considered.")
++    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occurring more than this many times won't be considered.")
+     ("maxReadOcc,w", po::value<uint32_t>(&(sopt.maxReadOccs))->default_value(100), "Reads \"mapping\" to more than this many places won't be considered.")
+     ("noEffectiveLengthCorrection", po::bool_switch(&(sopt.noEffectiveLengthCorrection))->default_value(false), "Disables "
+                         "effective length correction when computing the probability that a fragment was generated "
diff --git a/debian/patches/series b/debian/patches/series
index 7417274..121dc3d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,4 +3,3 @@ jellyfish-update
 cmake-adj
 drop-mathjax
 cmake-typo-fixes
-spelling-fixes
diff --git a/debian/patches/spelling-fixes b/debian/patches/spelling-fixes
deleted file mode 100644
index 2a78659..0000000
--- a/debian/patches/spelling-fixes
+++ /dev/null
@@ -1,11 +0,0 @@
---- salmon.orig/src/SalmonQuantify.cpp
-+++ salmon/src/SalmonQuantify.cpp
-@@ -2928,7 +2928,7 @@
-                                         "many reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should "
-                                         "not be too large if you wish to keep a low memory usage, but setting it large enough can substantially speed up "
-                                         "inference on \"small\" files that contain only a few million reads.")
--    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occuring more than this many times won't be considered.")
-+    ("maxOcc,m", po::value<int>(&(memOptions->max_occ))->default_value(200), "(S)MEMs occurring more than this many times won't be considered.")
-     ("maxReadOcc,w", po::value<uint32_t>(&(sopt.maxReadOccs))->default_value(100), "Reads \"mapping\" to more than this many places won't be considered.")
-     ("noEffectiveLengthCorrection", po::bool_switch(&(sopt.noEffectiveLengthCorrection))->default_value(false), "Disables "
-                         "effective length correction when computing the probability that a fragment was generated "

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/salmon.git