From bf0a50e5eef0c9eb43638eab881019494002948b Mon Sep 17 00:00:00 2001 From: Sarvesh Prakash Nikumbh Date: Mon, 31 Jul 2017 20:58:19 +0200 Subject: [PATCH] a minor spelling error rectified --- readFastaSequences.m | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/readFastaSequences.m b/readFastaSequences.m index 7014b64..d5a64c4 100644 --- a/readFastaSequences.m +++ b/readFastaSequences.m @@ -1,4 +1,4 @@ -function [nSeqs, ommittedIndices, passFasta] = readFastaSequences(txt, segmentSizeInBps, givenNSeqs, outputFolder, debugLevel, debugMsgLocation) +function [nSeqs, omittedIndices, passFasta] = readFastaSequences(txt, segmentSizeInBps, givenNSeqs, outputFolder, debugLevel, debugMsgLocation) % READFASTASEQUENCES % @@ -46,11 +46,11 @@ fasta.legend = cell(1, givenNSeqs); fasta.sequence = cell(1, givenNSeqs); i=0; -ommittedIndices = []; +omittedIndices = []; fasta.title=[txt,', read: ', date]; % Read Sequences and their FASTA legends fid=fopen(txt,'r'); -ofid=fopen(strcat(outputFolder, '/ommittedFastaIds.txt'), 'a'); +ofid=fopen(strcat(outputFolder, '/omittedFastaIds.txt'), 'a'); fprintf(ofid, '----%s---%s----\n\n', fprintf('%s',datetime('now')), txt); lengths = []; while i < givenNSeqs % feof(fid)==0 @@ -64,7 +64,7 @@ if lengths(end) >= segmentSizeInBps fasta.sequence{i}=[fasta.sequence{i},upper(lineRead)]; else % we omit that sequence - ommittedIndices = [ommittedIndices i]; + omittedIndices = [omittedIndices i]; fprintf(ofid, '%d\t%s', i, fasta.legend{i}); fprintf(ofid, '\n'); end @@ -81,7 +81,7 @@ passFasta = fasta; if size(ineligibleLengths, 2) > 0 - logMessages(debugMsgLocation, sprintf('%d sequence(s) have been ommitted as they are shorter than the segment-size specified. Check ommittedFastaIds.txt\n', length(ineligibleIndices)), debugLevel); + logMessages(debugMsgLocation, sprintf('%d sequence(s) have been omitted as they are shorter than the segment-size specified. Check omittedFastaIds.txt\n', length(ineligibleIndices)), debugLevel); % Change to what would be passed, if it is different than 'fasta' above nSeqs = length(find(lengths >= segmentSizeInBps)); passFasta.sequence = cell(1, nSeqs);