[med-svn] [trinityrnaseq] 01/01: fix typos & update patch descriptions

[Michael Crusoe]

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

commit d1fb59ce4126fce2baec5e56ed79c13f20781b8e
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sun Jan 24 10:25:25 2016 -0800

    fix typos & update patch descriptions
---
 debian/TODO                                     |  3 ---
 debian/patches/adjust-trimmomatic-adapters-path |  2 +-
 debian/patches/noExitTester                     |  3 ++-
 debian/patches/series                           |  1 +
 debian/patches/spelling                         | 35 +++++++++++++++++++++++++
 5 files changed, 39 insertions(+), 5 deletions(-)

diff --git a/debian/TODO b/debian/TODO
index 33b6173..7d8c4f8 100644
--- a/debian/TODO
+++ b/debian/TODO
@@ -1,4 +1 @@
-- package kallisto
-- trinityrnaseq: spelling-error-in-binary usr/lib/trinityrnaseq/Inchworm/bin/fastaToKmerCoverageStats occurences occurrences
-- trinityrnaseq: spelling-error-in-binary usr/lib/trinityrnaseq/Inchworm/bin/inchworm occurences occurrences
 - hardening-no-fortify-functions usr/lib/trinityrnaseq/Inchworm/bin/inchworm
diff --git a/debian/patches/adjust-trimmomatic-adapters-path b/debian/patches/adjust-trimmomatic-adapters-path
index e787ec8..c60d767 100644
--- a/debian/patches/adjust-trimmomatic-adapters-path
+++ b/debian/patches/adjust-trimmomatic-adapters-path
@@ -7,7 +7,7 @@ Description: Match the Debian's path
  my $PARAFLY = "/usr/bin/ParaFly";
  my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
 -my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
-+my $TRIMMOMATIC_DIR = "/usr/share/Trimmomatic";
++my $TRIMMOMATIC_DIR = "/usr/share/trimmomatic";
  
  $ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
  
diff --git a/debian/patches/noExitTester b/debian/patches/noExitTester
index c2f0759..123ba06 100644
--- a/debian/patches/noExitTester
+++ b/debian/patches/noExitTester
@@ -1,4 +1,5 @@
-Description:NoExitTester
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: Don't try to test Java
 --- trinityrnaseq.orig/Trinity
 +++ trinityrnaseq/Trinity
 @@ -2260,32 +2260,6 @@
diff --git a/debian/patches/series b/debian/patches/series
index 0466480..7ec61e4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+spelling
 skip-kallisto-deseq2-tests
 hashbang
 chrysalis-make-tweak
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..1dcc7f2
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,35 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: occurences -> occurrences
+--- trinityrnaseq.orig/Inchworm/src/IRKE.cpp
++++ trinityrnaseq/Inchworm/src/IRKE.cpp
+@@ -93,7 +93,7 @@
+   	record_counter[i] = 0;
+   }
+ 
+-	cerr << "-reading Kmer occurences..." << endl;
++	cerr << "-reading Kmer occurrences..." << endl;
+ 	start = time(NULL);
+ 
+ 	Fasta_reader fasta_reader(fasta_filename);
+--- trinityrnaseq.orig/Chrysalis/MakeDepend.cc
++++ trinityrnaseq/Chrysalis/MakeDepend.cc
+@@ -420,7 +420,7 @@
+ 
+   // The vector of pairs count_per_provider[] simply reverses the map
+   // provider_counts[], copying each map element B->n to an ordered pair (n,B),
+-  // so that the resulting vector can be sorted by number of occurences, rather
++  // so that the resulting vector can be sorted by number of occurrences, rather
+   // than provider name.  (Why not build the mapping as a vector in the first
+   // place?  Efficiency: keeping the vector sorted while building up the map
+   // would require a lot of copying of data everytime a new provider name was
+--- trinityrnaseq.orig/Inchworm/src/fastaToKmerCoverageStats.cpp
++++ trinityrnaseq/Inchworm/src/fastaToKmerCoverageStats.cpp
+@@ -168,7 +168,7 @@
+     for (int i = 0; i < omp_get_max_threads(); i++) {
+         record_counter[i] = 0;
+     }
+-    cerr << "-reading Kmer occurences..." << endl;
++    cerr << "-reading Kmer occurrences..." << endl;
+     start = time(NULL);
+     Fasta_reader fasta_reader(kmers_fasta_file);
+     #pragma omp parallel private (myTid)

-- 
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