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Author: Michael R. Crusoe
Description: typo fix
Forwarded: https://github.com/amplab/snap/pull/66
--- snap-aligner.orig/SNAPLib/AlignerOptions.cpp
+++ snap-aligner/SNAPLib/AlignerOptions.cpp
@@ -145,7 +145,7 @@
" -R Specify the entire read group line for the SAM/BAM output. This must include an ID tag. If it doesn't start with\n"
" '@RG' SNAP will add that. Specify tabs by \\t. Two backslashes will generate a single backslash.\n"
" backslash followed by anything else is illegal. So, '-R @RG\\tID:foo\\tDS:my data' would generate reads\n"
- " with defualt tag foo, and an @RG line that also included the DS:my data field.\n"
+ " with default tag foo, and an @RG line that also included the DS:my data field.\n"
" -sa Include reads from SAM or BAM files with the secondary (0x100) or supplementary (0x800) flag set; default is to drop them.\n"
" -om Output multiple alignments. Takes as a parameter the maximum extra edit distance relative to the best alignment\n"
" to allow for secondary alignments\n"
@@ -173,7 +173,7 @@
" -dp Edit distance as a percentage of read length (single only, overrides -d)\n"
#endif
" -nu No Ukkonen: don't reduce edit distance search based on prior candidates. This option is purely for\n"
- " evalutating the performance effect of using Ukkonen's algorithm rather than Smith-Waterman, and specifying\n"
+ " evaluating the performance effect of using Ukkonen's algorithm rather than Smith-Waterman, and specifying\n"
" it will slow down execution without improving the alignments.\n"
" -no No Ordering: don't order the evalutation of reads so as to select more likely candidates first. This option\n"
" is purely for evaluating the performance effect of the read evaluation order, and specifying it will slow\n"
@@ -208,7 +208,7 @@
WriteErrorMessage("When specifying an input or output file, you can simply list the filename, in which case\n"
"SNAP will infer the type of the file from the file extension (.sam or .bam for example),\n"
- "or you can explicitly specify the file type by preceeding the filename with one of the\n"
+ "or you can explicitly specify the file type by preceding the filename with one of the\n"
" following type specifiers (which are case sensitive):\n"
" -fastq\n"
" -compressedFastq\n"
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