preprocessing step doesn't produce bowtie2 compatable fasta reference from input long fastq

[nickschurch]

hercules help suggests that it can use a fastq as input for the long reads. the preprocessing step works fine, but then the suggested bowtie2 steps fail because bowtie2-build requires a fasta reference and compressed_long is still a fastq (albeit one with all the quality information removed).

[canfirtina]

Hello Nick,

Thank you for the notice. Yes, I noticed the problem. It is because the function I wrote ignores the extension of a file as follows:

hercules/src/main.cpp

Lines 1201 to 1206 in b232b01

	std::string getBasename(std::string fullPath){
	size_t baseStart = fullPath.rfind(SEPERATOR, fullPath.length());
	if( baseStart != std::string::npos)
	return fullPath.substr(baseStart+1, fullPath.length() - baseStart);
	return fullPath;
	}

It will be fixed in the next commit. For now, you can simply change the file extension of the compressed file from fastq to fasta and try running bowtie2-build