Package 

Class OutFormat

  • All Implemented Interfaces:
    org.veupathdb.lib.blast.serial.BlastField 
    
public final class OutFormat
 implements BlastField

    -outfmt <String>

    Alignment view options:

    0  = Pairwise
1  = Query-anchored showing identities
2  = Query-anchored no identities
3  = Flat query-anchored showing identities
4  = Flat query-anchored no identities
5  = BLAST XML
6  = Tabular
7  = Tabular with comment lines
8  = Seqalign (Text ASN.1)
9  = Seqalign (Binary ASN.1)
10 = Comma-separated values
11 = BLAST archive (ASN.1)
12 = Seqalign (JSON)
13 = Multiple-file BLAST JSON
14 = Multiple-file BLAST XML2
15 = Single-file BLAST JSON
16 = Single-file BLAST XML2
17 = Sequence Alignment/Map (SAM)
18 = Organism Report

    Options 6, 7, 10 and 17 can be additionally configured to produce a custom format specified by space delimited format specifiers, or in the case of options 6, 7, and 10, by a token specified by the delim keyword. E.g.: "17 delim=@ qacc sacc score".

    The delim keyword must appear after the numeric output format specification.

    The supported format specifiers for options 6, 7 and 10 are:

    qseqid     means Query Seq-id
qgi        means Query GI
qacc       means Query accesion
qaccver    means Query accesion.version
qlen       means Query sequence length
sseqid     means Subject Seq-id
sallseqid  means All subject Seq-id(s), separated by a ';'
sgi        means Subject GI
sallgi     means All subject GIs
sacc       means Subject accession
saccver    means Subject accession.version
sallacc    means All subject accessions
slen       means Subject sequence length
qstart     means Start of alignment in query
qend       means End of alignment in query
sstart     means Start of alignment in subject
send       means End of alignment in subject
qseq       means Aligned part of query sequence
sseq       means Aligned part of subject sequence
evalue     means Expect value
bitscore   means Bit score
score      means Raw score
length     means Alignment length
pident     means Percentage of identical matches
nident     means Number of identical matches
mismatch   means Number of mismatches
positive   means Number of positive-scoring matches
gapopen    means Number of gap openings
gaps       means Total number of gaps
ppos       means Percentage of positive-scoring matches
frames     means Query and subject frames separated by a '/'
qframe     means Query frame
sframe     means Subject frame
btop       means Blast traceback operations (BTOP)
staxid     means Subject Taxonomy ID
ssciname   means Subject Scientific Name
scomname   means Subject Common Name
sblastname means Subject Blast Name
sskingdom  means Subject Super Kingdom
staxids    means unique Subject Taxonomy ID(s), separated by a ';'
                 (in numerical order)
sscinames  means unique Subject Scientific Name(s), separated by a ';'
scomnames  means unique Subject Common Name(s), separated by a ';'
sblastnamesmeans unique Subject Blast Name(s), separated by a ';'
                 (in alphabetical order)
sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
                 (in alphabetical order)
stitle     means Subject Title
salltitles means All Subject Title(s), separated by a '<>'
sstrand    means Subject Strand
qcovs      means Query Coverage Per Subject
qcovhsp    means Query Coverage Per HSP
qcovus     means Query Coverage Per Unique Subject (blastn only)

    When not provided, the default value is:

    qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore

    which is equivalent to the keyword std

    The supported format specifier for option 17 is:

    SQ means Include Sequence Data
SR means Subject as Reference Seq

    Default = 0