From: Michael R. Crusoe <crusoe@debian.org>
Subject: spelling/grammer fixes
Forwarded: https://github.com/amplab/snap/pull/128

--- snap-aligner.orig/SNAPLib/AlignerOptions.cpp
+++ snap-aligner/SNAPLib/AlignerOptions.cpp
@@ -170,7 +170,7 @@
             "  -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"
--- snap-aligner.orig/SNAPLib/GenomeIndex.cpp
+++ snap-aligner/SNAPLib/GenomeIndex.cpp
@@ -83,9 +83,9 @@
         "                   In particular, this will generally use less memory than the index will use once it's built, so if this doesn't work you\n"
         "                   won't be able to use the index anyway. However, if you've got sufficient memory to begin with, this option will just\n"
         "                   slow down the index build by doing extra, useless IO.\n"
-        " -AutoAlt-         Don't automatically mark ALT contigs.  Otherwise, any contig thats name ends in '_alt' (regardless of captialization) or starts\n"
+        " -AutoAlt-         Don't automatically mark ALT contigs.  Otherwise, any contig whose name ends in '_alt' (regardless of captialization) or starts\n"
         "                   with HLA- will be marked ALT.  Others will not.\n"
-		" -maxAltContigSize Specify a size at or below which all contigs are automatically marked ALT, unless overriden by name using the args below\n"
+		" -maxAltContigSize Specify a size at or below which all contigs are automatically marked ALT, unless overridden by name using the args below\n"
 		" -altContigName    Specify the (case independent) name of an alt to mark a contig.  You can supply this parameter as often as you'd like\n"
 		" -altContigFile    Specify the name of a file with a list of alt contig names, one per line.  You may specify this as often as you'd like\n"
 		" -nonAltContigName Specify the name of a contig that's not an alt, regardless of its size\n"
