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

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

qfilt -Q 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 retain homopolymers/don't skip ambigs)
    5' tag:              ATATCGCGAGGA
    max tag mismatches:  0

run summary:
    original reads:      305
    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

-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, a low q-score causes reads to be split,
              otherwise they are truncated;
              if the second bit is set, low q-score homopolymers are tolerated;
              and if the highest bit is set, low q-score 'N's are tolerated

-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)