<commit_before>// SeqInput.h

#ifndef FLEXBAR_SEQINPUT_H
#define FLEXBAR_SEQINPUT_H

#include <seqan/seq_io.h>
#include "QualTrimming.h"


template <typename TSeqStr, typename TString>
class SeqInput {

private:
	
	seqan::SeqFileIn seqFileIn;
	const flexbar::QualTrimType m_qtrim;
	const flexbar::FileFormat m_format;
	// typedef seqan::String<char, seqan::MMap<> > TMMapString;
	
	const bool m_preProcess, m_useStdin, m_qtrimPostRm;
	const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize;
	tbb::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred;
	<commit_msg>Cleanup<commit_after>// SeqInput.h

#ifndef FLEXBAR_SEQINPUT_H
#define FLEXBAR_SEQINPUT_H

#include <seqan/seq_io.h>
#include "QualTrimming.h"


template <typename TSeqStr, typename TString>
class SeqInput {

private:
	
	seqan::SeqFileIn seqFileIn;
	const flexbar::QualTrimType m_qtrim;
	const flexbar::FileFormat m_format;
	
	const bool m_preProcess, m_useStdin, m_qtrimPostRm;
	const int m_maxUncalled, m_preTrimBegin, m_preTrimEnd, m_qtrimThresh, m_qtrimWinSize;
	tbb::atomic<unsigned long> m_nrReads, m_nrChars, m_nLowPhred;
	
{'fraction_non_alphanumeric': 0.09228039041703638, 'fraction_numerical': 0.0, 'mean_word_length': 6.943661971830986, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1723258', 'n_tokens_mistral': 481, 'n_tokens_neox': 444, 'n_words': 90}