have matlab use global executables

1 files changed, 4 insertions, 14 deletions

diff --git a/src/matlab/quikrCustomTrained.m b/src/matlab/quikrCustomTrained.m
index b58aa31..c7961c7 100644
--- a/src/matlab/quikrCustomTrained.m
+++ b/src/matlab/quikrCustomTrained.m
@@ -15,19 +15,9 @@ if rws~=4^k
     error('Wrong k-mer size for input training matrix');

 end

 

-if (isunix && not(ismac))

-    [status, counts]=unix([sprintf('./count-linux -r %d -1 -u ',k) ' ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels.

-     if status ~= 0

-        error('./count-linux failed: ensure count-linux is an executable. Try chmod a+rx count-linux. Be sure matlab/octave is in the same directory as count-linux');

-    end

-elseif ismac

-    [status, counts]=unix([sprintf('./count-osx -r %d -1 -u ',k) ' ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels.

-    if status ~= 0

-        error('./count-osx failed: ensure count-linux is an executable. Try chmod a+rx count-osx. Be sure matlab/octave is in the same directory as count-osx');

-    end

-elseif ispc

-   error('Windows is not yet supported');

-end

+[status, counts]=unix(['count-kmers -r 6 -1 -u ' inputfasta]); %count the 6-mers in the fasta file, in the forward direction, return the counts without labels

+if status ~= 0

+  error('count-kmers failed: ensure count-kmers is in your path.');

 

 counts=textscan(counts,'%f'); %read them in as floats.

 counts=counts{:};

@@ -39,4 +29,4 @@ Aaux=[ones(1,clumns);lambda*trainingmatrix]; %form the k-mer sensing matrix
 warning off

 xstar=lsqnonneg(Aaux,yaux); %perform the non-negative lease squares

 warning on

-xstar=xstar/sum(xstar); %return the results as a probability vector 
\ No newline at end of file
+xstar=xstar/sum(xstar); %return the results as a probability vector