cmake [-DINSTALL_PREFIX=/install/path (default=/usr/local)] .
make install

qfilt [-h] [-v] [-o OUTPUT] [-q QSCORE] [-l LENGTH] [-m MODE] [-T PREFIX] [-t MISMATCH] (-F FASTQ | -Q FASTA QUAL)

qfilt -F data/test.fna data/test.qual -q 15 -l 30 -T ATATCGCGAGGA

run settings:
	input fasta:         data/test.fna
	input qual:          data/test.qual
	min q-score:         15
	min fragment length: 30
	run mode:            0 (truncate/don't tolerate homopolymers/don't tolerate ambigs)
	5' tag:              ATATCGCGAGGA
	max tag mismatches:  0

run summary:
	total bases       :  29570
	original reads    :  305
	q10               :  0.995502
	q20               :  0.860298
	q30               :  0.728745
	mean q-score      :  33.2273
	contributing reads:  5
	retained fragments:  5

original read length distribution:
	mean:                96.9508
	median:              77
	variance             3743.03
	standard deviation:  61.1803
	min:                 49
	2.5%:                54
	97.5%:               332
	max:                 497

retained fragment length distribution:
	mean:                41
	median:              37
	variance             72.5
	standard deviation:  8.51469
	min:                 33
	2.5%:                33
	97.5%:               54
	max:                 54

>GM98SRO01B77KU rank=0000671 x=796.0 y=1996.0 length=58
CCACGCGTATCGATGTCGACTTTTTTTTCTTTTCTTACATAGTAG
>GM98SRO01BA3RP rank=0000953 x=419.5 y=1603.5 length=87
CTGATGCTGCACCAACTGTACTCCCTCGCGATA
>GM98SRO01E1BKW rank=0001233 x=1948.0 y=846.0 length=66
TACAGTTGGTGCAGCATCAGAAAAGTACGACATCGATACGCGTGGTCCTCGCGA
>GM98SRO01DVVNY rank=0001304 x=1476.0 y=636.5 length=84
ACGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA
>GM98SRO01D6FIX rank=0001416 x=1596.0 y=1415.0 length=91
CGGCTGATGCTGCACCAACTGTACTCCCTCGCGATA

optional arguments:
-h, --help               show this help message and exit
-v, --version            show version and exit
-o OUTPUT                direct retained fragments to a file named OUTPUT (default=stdout)
-q QSCORE                minimum per-base quality score below which a read will be split
                         or truncated (default=20)
-l LENGTH                minimum retained fragment LENGTH (default=50)
-m MODE                  MODE is a 3-bitmask (an integer in [0-7], default=0):
                         if the lowest bit is set, it is like passing -s;
                         if the middle bit is set, it is like passing -p;
                         and if the highest bit is set, it is like passing -a
-s                       when encountering a low q-score, split instead of truncate
-p                       tolerate low q-score homopolymeric regions
-a                       tolerate low q-score ambiguous nucleotides
-T PREFIX                if supplied, only reads with this PREFIX are retained,
                         and the PREFIX is stripped from each contributing read
-t MISMATCH              if PREFIX is supplied, prefix matching tolerates at most
                         MISMATCH mismatches (default=0)
-f FORMAT                output in FASTA or FASTQ format (default=FASTA)
-j                       output run diagnostics to stderr as JSON (default is to write ASCII text)