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Fix some typos #311

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Fix some typos #311

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2 changes: 1 addition & 1 deletion NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -1198,7 +1198,7 @@ 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)
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10 changes: 5 additions & 5 deletions bwa.1
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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 :
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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;)*/
_
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4 changes: 2 additions & 2 deletions bwamem.h
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Expand Up @@ -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
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