RUN_LOG

# 0:05
# project architecture

# 0:18
# main data structures used in project:
# Reference Kmers Database, Reads Kmers Database

# 0:35
# classes used in program:
# Kmer, Read, Reference

# 0:47
# code example - Class Read

# 0:58 
# Class Alignment

# 1:09
# code example - important function in project
# map_reads() function from Class Alignment

# 1:22 
# data structures comparison
# explanation why data structures were chosen

# 1:41
# example of principals learned in course:
# using functional programming and OOP

# 1:48
# loading FASTA/Q files
# using generators

# 1:56
# loading\ dumping ALN\ KDB files
# explaining the files structure
# using pickle and gzip modules

# 2:08
# extension - quality
# explanation the method of implementation

# 2:22
# extension - reverse
# explanation the method of implementation

# 2:39
# extension - coverage
# explanation the method of implementation

# 2:54
# extension - similarity
# explanation the method of implementation

# 3:04
# example of extension EXTSIM:
python3 main.py -t dumpref -g ref_extsim.fa -k 31 --filter-similar

# 3:44
# example of extension EXTQUALITY:
python3 main.py -t dumpalign -g ref_quality.fa -k 31 --reads reads_quality.fq --min-read-quality 29

# 4:14
# example of extension EXTQUALITY:
python3 main.py -t dumpalign -g ref_quality.fa -k 31 --reads reads_quality.fq --max-genomes 2

# 4:25
# program's usage instructions:
python3 main.py --help

# 4:30
# example of extension EXTREVCOMP:
python3 main.py -t dumpalign -g ref_reverse.fa -k 31 --reads reads_reverse.fq --reverse-complement