From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Fix spelling
Forwarded: https://github.com/bcgsc/abyss/pull/282

Spelling typos found via the Debian lintian checks
--- abyss.orig/Consensus/Consensus.cpp
+++ abyss/Consensus/Consensus.cpp
@@ -453,7 +453,7 @@
 		} else if (opt::verbose > 0) {
 			cerr << "warning: Contig " << it->first
 				<< " was not supported by a complete read "
-				"and was ommited.\n";
+				"and was omitted.\n";
 		}
 	}
 }
--- abyss.orig/dialign/parameters.c
+++ abyss/dialign/parameters.c
@@ -300,7 +300,7 @@
 	printf("  -n\tmaximum number of consecutive positions for window containing\n     \tlow scoring positions \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 4]\n");
 	printf("  -g\tglobal minimum fragment length for stop criterion \n \t\t[DEFAULT PROTEIN: 40] \n\t\t[DEFAULT DNA: 40]\n");
 	printf("  -m\tminimal allowed average score in frag window containing low \n     \tscoring positions \n \t\t[DEFAULT PROTEIN: 4.0]\n\t\t[DEFAULT DNA: 0.25]\n");
-	printf("  -o\twether overlap weights are calculated or not [DEFAULT 0]\n");
+	printf("  -o\twhether overlap weights are calculated or not [DEFAULT 0]\n");
 	printf("  -f\tminimum fragment length [DEFAULT 1]\n");
 	printf("  -r\tthreshold weight to consider the fragment at all [DEFAULT 0.0]\n");
 	printf("  -u\t[DEFAULT 0]\n");
--- abyss.orig/dialign/parameters.h
+++ abyss/dialign/parameters.h
@@ -90,7 +90,7 @@
 	 *
 	 *****************************/
 
-	// wether overlap weights are calculated or not
+	// whether overlap weights are calculated or not
 	int DO_OVERLAP; // = 0;
 
 	// minimum diag length
--- abyss.orig/SimpleGraph/SimpleGraph.cpp
+++ abyss/SimpleGraph/SimpleGraph.cpp
@@ -806,7 +806,7 @@
 			<< g_minNumPairsUsed << ".\n";
 		if (g_minNumPairs < g_minNumPairsUsed)
 			cout << "Consider increasing the number of pairs "
-				"threshold paramter, n, to " << g_minNumPairsUsed
+				"threshold parameter, n, to " << g_minNumPairsUsed
 				<< ".\n";
 	}
 
--- abyss.orig/DataLayer/abyss-tofastq.cc
+++ abyss/DataLayer/abyss-tofastq.cc
@@ -34,8 +34,8 @@
 "\n"
 "      --cat               concatenate the records [default]\n"
 "  -i, --interleave        interleave the records\n"
-"      --fastq             ouput FASTQ format [default]\n"
-"      --fasta             ouput FASTA format\n"
+"      --fastq             output FASTQ format [default]\n"
+"      --fasta             output FASTA format\n"
 "      --bx                copy SAM BX tag to output FASTA comment\n"
 "      --chastity          discard unchaste reads [default]\n"
 "      --no-chastity       do not discard unchaste reads\n"
--- abyss.orig/Konnector/konnector.cc
+++ abyss/Konnector/konnector.cc
@@ -128,7 +128,7 @@
 "                               use 'nolimit' for no limit [nolimit]\n"
 "\n"
 "  Note: --max-branches was not effective for truncating expensive searches,\n"
-"  and has been superceded by the --max-cost option.\n"
+"  and has been superseded by the --max-cost option.\n"
 "\n"
 "Report bugs to <" PACKAGE_BUGREPORT ">.\n";
 
@@ -864,7 +864,7 @@
 
 	updateCounters(params, result);
 
-	/* ouput merged / unmerged reads */
+	/* output merged / unmerged reads */
 
 	if (result.pathResult == FOUND_PATH &&
 		!exceedsMismatchThresholds(params, result)) {
--- abyss.orig/Sealer/sealer.cc
+++ abyss/Sealer/sealer.cc
@@ -124,12 +124,12 @@
 "  -F, --max-frag=N             max fragment size in base pairs\n"
 "\n"
 "  Note 1: --max-branches was not effective for truncating expensive searches,\n"
-"  and has been superceded by the --max-cost option.\n"
+"  and has been superseded by the --max-cost option.\n"
 "\n"
 "  Note 2: --max-frag was formerly used to determine the maximum gap\n"
 "  size that abyss-sealer would attempt to close, according to the formula\n"
 "  max_gap_size = max_frag - 2 * flank_length, where flank_length is\n"
-"  determined by the -L option.  --max-frag is superceded by the more\n"
+"  determined by the -L option.  --max-frag is superseded by the more\n"
 "  intuitive -G (--max-gap-length) option. The related option --min-frag\n"
 "  does not seem to have any practical use.\n"
 "\n"
--- abyss.orig/doc/abyss-pe.1
+++ abyss/doc/abyss-pe.1
@@ -24,7 +24,7 @@
 .TP
 .B lib
 a quoted list of whitespace-separated paired-end library names. Use
-this varible when assembling data from multiple paired-end libraries.
+this variable when assembling data from multiple paired-end libraries.
 For each library name in lib, the user must define a variable on
 the command line with the same name, which indicates the read files for
 that library. See \fBEXAMPLES\fR below for a concrete example of usage.
