Spelling fixes

Gibbs.cpp

@@ -432,7 +432,7 @@ int main(int argc, char* argv[]) {
     printf("- One isoform's prior per line\n");
     printf("- Priors must be in the same order as in the .ti file\n");
     printf("- Priors for those to-be-omitted isoforms must be included as well\n");
-    printf("- Comments can be added after prior seperated by space(s)\n");
+    printf("- Comments can be added after prior separated by space(s)\n");
 		exit(-1);
 	}
 

pRSEM/File.py

@@ -10,7 +10,7 @@ def __init__(self):
     self.fullname = None  ## file's full name, include dir, base, and all ext
     self.is_gz    = None  ## if file is gzipped
     self.dirname  = None  ## directory name
-    self.basename = None  ## base name sans all extension seperated by dot
+    self.basename = None  ## base name sans all extension separated by dot
     self.filename_sans_ext = None ## no path, no last extension sep by dot
 
 

rsem-calculate-expression

@@ -1125,7 +1125,7 @@ Using a logistic regression to combine TSS signals from multiple complementary d
 
 =back
 
-Parameters for all the above models are learned from a training set. For detailed explainations, please see prior-enhanced RSEM's paper. (Default: 'pk')
+Parameters for all the above models are learned from a training set. For detailed explanations, please see prior-enhanced RSEM's paper. (Default: 'pk')
 
 =back
 

rsem-plot-transcript-wiggles

@@ -149,7 +149,7 @@ This program generates transcript wiggle plots and outputs them in a pdf file. T
 
 =item B<output_plot_file>
 
-This is a pdf file containing all plots generated. If a list of transcript ids is provided, each page display at most 6 plots in 3 rows and 2 columns. If gene ids are provided, each page display a gene. The gene's id is showed at the top and all its transcripts' wiggle plots are showed in this page. The arrangment of plots is determined automatically. For each transcript wiggle plot, the transcript id is displayed as title. x-axis is position in the transcript and y-axis is read depth. If allele-specific expression is calculated, the basin unit becomes an allele-specific transcript and transcript ids and gene ids can be used to group allele-specific transcripts.
+This is a pdf file containing all plots generated. If a list of transcript ids is provided, each page display at most 6 plots in 3 rows and 2 columns. If gene ids are provided, each page display a gene. The gene's id is showed at the top and all its transcripts' wiggle plots are showed in this page. The arrangement of plots is determined automatically. For each transcript wiggle plot, the transcript id is displayed as title. x-axis is position in the transcript and y-axis is read depth. If allele-specific expression is calculated, the basin unit becomes an allele-specific transcript and transcript ids and gene ids can be used to group allele-specific transcripts.
 
 =item B<sample_name.transcript.sorted.bam and sample_name.transcript.readdepth>
 

rsem-prepare-reference

@@ -329,7 +329,7 @@ Build STAR indices. (Default: off)
 
 =item B<--star-path> <path>
 
-The path to STAR's executable. (Default: the path to STAR executable is assumed to be in user's PATH environment varaible)
+The path to STAR's executable. (Default: the path to STAR executable is assumed to be in user's PATH environment variable)
 
 =item B<--star-sjdboverhang> <int>