magicblast options

gistfile1.txt

Careful!
version 1.2 does NOT return unaligned reads
        1.3 however, DOES return unaligned reads. Need to use the '-no_unaligned' option

$ magicblast -version
magicblast: 1.2.0
 Package: magicblast 1.2.0, build Feb 21 2017 15:46:57

$ magicblast -h
  magicblast [-h] [-help] [-db database_name] [-gilist filename]
    [-seqidlist filename] [-negative_gilist filename]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-gzo] [-word_size int_value] [-gapopen open_penalty]
    [-gapextend extend_penalty] [-perc_identity float_value]
    [-penalty penalty] [-lcase_masking] [-validate_seqs TF] [-infmt format]
    [-paired] [-query_mate infile] [-sra accession] [-parse_deflines TF]
    [-outfmt format] [-num_threads int_value] [-max_intron_length length]
    [-score num] [-splice TF] [-reftype type] [-limit_lookup TF]
    [-lookup_stride num] [-batch_size num] [-version]

$ ./magicblast -version
magicblast: 1.3.0
 Package: magicblast 1.3.0, build Sep 13 2017 15:43:18

$ ./magicblast -h
  magicblast [-h] [-help] [-db database_name] [-gilist filename]
    [-seqidlist filename] [-negative_gilist filename]
    [-negative_seqidlist filename] [-db_soft_mask filtering_algorithm]
    [-db_hard_mask filtering_algorithm] [-subject subject_input_file]
    [-subject_loc range] [-query input_file] [-out output_file] [-gzo]
    [-word_size int_value] [-gapopen open_penalty] [-gapextend extend_penalty]
    [-perc_identity float_value] [-penalty penalty] [-lcase_masking]
    [-validate_seqs TF] [-infmt format] [-paired] [-query_mate infile]
    [-sra accession] [-parse_deflines TF] [-sra_cache] [-outfmt format]
    [-no_query_id_trim] [-no_unaligned] [-num_threads int_value]
    [-max_intron_length length] [-score num] [-max_edit_dist num] [-splice TF]
    [-reftype type] [-limit_lookup TF] [-lookup_stride num] [-version]