Merge pull request #311 from mr-c/spelling

Fix some typos

Author: lh3

NEWS.md

@@ -1213,7 +1213,7 @@ Beta Release 0.1.4 (22 July, 2008)
 Beta Release 0.1.3 (21 July, 2008)
 ----------------------------------
 
-Improve the speed with some tricks on retrieving occurences. The results
+Improve the speed with some tricks on retrieving occurrences. The results
 should be exactly the same as that of 0.1.2.
 
 (0.1.3: 21 July 2008, r382)

bwa.1

@@ -202,7 +202,7 @@ yields fewer seeds, which leads to faster alignment speed but lower accuracy. [1
 .BI -c \ INT
 Discard a MEM if it has more than
 .I INT
-occurence in the genome. This is an insensitive parameter. [500]
+occurrence in the genome. This is an insensitive parameter. [500]
 .TP
 .BI -D \ FLOAT
 Drop chains shorter than
@@ -235,7 +235,7 @@ Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) *
 .TP
 .BI -O \ INT[,INT]
 Gap open penalty. If two numbers are specified, the first is the penalty of
-openning a deletion and the second for openning an insertion. [6]
+opening a deletion and the second for opening an insertion. [6]
 .TP
 .BI -E \ INT[,INT]
 Gap extension penalty. If two numbers are specified, the first is the penalty
@@ -260,7 +260,7 @@ two scores to determine whether we should force pairing. A larger value leads to
 more aggressive read pair. [17]
 .TP
 .BI -x \ STR
-Read type. Changes multiple parameters unless overriden [null]
+Read type. Changes multiple parameters unless overridden [null]
 .RS
 .TP 10
 .BR pacbio :
@@ -301,7 +301,7 @@ Write the output SAM file to
 For compatibility with other BWA commands, this option may also be given as
 .B -f
 .IR FILE .
-[standard ouptut]
+[standard output]
 .TP
 .B -q
  Don't reduce the mapping quality of split alignment of lower alignment score.
@@ -688,7 +688,7 @@ X1	Number of suboptimal hits found by BWA
 XN	Number of ambiguous bases in the referenece
 XM	Number of mismatches in the alignment
 XO	Number of gap opens
-XG	Number of gap extentions
+XG	Number of gap extensions
 XT	Type: Unique/Repeat/N/Mate-sw
 XA	Alternative hits; format: /(chr,pos,CIGAR,NM;)*/
 _

bwamem.h

@@ -66,8 +66,8 @@ typedef struct {
 	int min_chain_weight;
 	int max_chain_extend;
 	float split_factor;     // split into a seed if MEM is longer than min_seed_len*split_factor
-	int split_width;        // split into a seed if its occurence is smaller than this value
-	int max_occ;            // skip a seed if its occurence is larger than this value
+	int split_width;        // split into a seed if its occurrence is smaller than this value
+	int max_occ;            // skip a seed if its occurrence is larger than this value
 	int max_chain_gap;      // do not chain seed if it is max_chain_gap-bp away from the closest seed
 	int n_threads;          // number of threads
 	int chunk_size;         // process chunk_size-bp sequences in a batch