#ifndef _INPUT_BLC_H
#define _INPUT_BLC_H

#include <stdio.h>
#include <stdlib.h>

#include "subread.h"
#include "seek-zlib.h"
#include "hashtable.h"

int input_BLC_init( input_BLC_t * blc_input , char * data_dir );
int input_BLC_next_read( input_BLC_t * blc_input, char * readname , char * read, char * qual );
int input_BLC_tell ( input_BLC_t * blc_input , input_BLC_pos_t * pos );
int input_BLC_seek ( input_BLC_t * blc_input , input_BLC_pos_t * pos );
void input_BLC_close (input_BLC_t * blc_input);

int input_scBAM_init(input_scBAM_t * bam_input, char * bam_fname);
void input_scBAM_close(input_scBAM_t * bam_input);
void scBAM_seek(input_scBAM_t * bam_input, input_scBAM_pos_t * pos);
void scBAM_tell(input_scBAM_t * bam_input, input_scBAM_pos_t * pos);
int scBAM_next_read(input_scBAM_t * bam_input, char * readname , char * read, char * qual );

int input_mFQ_init( input_mFQ_t * fqs_input, char ** files1, char ** files2, char** files3, int total_files );
int input_mFQ_init_by_one_string(input_mFQ_t * fqs_input, char * three_paired_fqnames);
int input_mFQ_next_read(input_mFQ_t * fqs_input, char * readname , char * read, char * qual );
int input_mFQ_tell(input_mFQ_t * fqs_input, input_mFQ_pos_t * pos );
int input_mFQ_seek(input_mFQ_t * fqs_input, input_mFQ_pos_t * pos );
void input_mFQ_close(input_mFQ_t * fqs_input);

// "cached BCL" maintains a chunk of reads; it decompresses 
int cacheBCL_init( cache_BCL_t * cache_input, char * data_dir, int reads_in_chunk, int all_threads );
int cacheBCL_next_read(  cache_BCL_t * cache_input, char * read_name, char * seq, char * qual, srInt_64 * read_number_in_all);
int cacheBCL_next_readbin(cache_BCL_t * cache_input, int * readlane, char readbin[BCL_READBIN_ITEMS_LOCAL][BCL_READBIN_SIZE], int max_readbin_buffer, srInt_64 * start_allread_no);

int cacheBCL_go_chunk_start( cache_BCL_t * blc_input );
int cacheBCL_go_chunk_end( cache_BCL_t * blc_input );
void cacheBCL_close ( cache_BCL_t * blc_input );

// it returns a hashtable : sample name -> [ ( "ACGTAATT", 1 ), ( "CGTTATGG", 2 ), ... ]
// The hashtable can be simply destroyed and all contents are deallocated automatically
// It returns NULL if no sample sheet is found
HashTable * input_BLC_parse_SampleSheet(char * fname);

// It returns a list of barcodes (not the barcode conversation table)
// It returns NULL if no list is found
// The arraylist can be simply destroyed and all contents are deallocated automatically
ArrayList * input_BLC_parse_CellBarcodes(char * fname);
int hamming_dist_ATGC_max1_2p(char* s1, char* s2 );
int hamming_dist_ATGC_max1(char* s1, char* s2 );
int hamming_dist_ATGC_max2(char* s1, char* s2 );
int hamming_dist_ATGC_max3(char* s1, char* s2 );

// returns -1 if error, or 0 if no error.
int cacheBCL_quality_test(int is_FASTQ_input, char * datadir, HashTable * sample_sheet_table, ArrayList * cell_barcode_list, int testing_reads, int * tested_reads, int * valid_sample_index, int * valid_cell_barcode);
#endif
