From fc0f77d5ec6dc4af32443918cc6ff780a81b6ea7 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 4 Feb 2021 16:05:52 +0100 Subject: [PATCH] Fix some typos --- NEWS.md | 2 +- bwa.1 | 10 +++++----- bwamem.h | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/NEWS.md b/NEWS.md index 151e024b..fcf06ee4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -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) diff --git a/bwa.1 b/bwa.1 index d30ac331..6ee1dbf7 100644 --- a/bwa.1 +++ b/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;)*/ _ diff --git a/bwamem.h b/bwamem.h index 0a0e3bb4..a518aaf5 100644 --- a/bwamem.h +++ b/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