| Input: |
| -A |
| |
--accession <accession> |
Replaces accession derived from <path> in filename(s) and
deflines (only for single table dump) |
|
|
--table <table-name> |
Table name within cSRA object, default is 'SEQUENCE' |
| Processing: |
| Read Splitting. Sequence data may be used in raw
form or split into individual reads |
|
|
--split-spot |
Split spots into individual reads |
| Full Spot Filters. Applied to the full spot
independently of --split-spot |
| -N |
| |
--minSpotId <rowid> |
Minimum spot id |
| -X |
| |
--maxSpotId <rowid> |
Maximum spot id |
|
|
--spot-groups <[list]> |
Filter by SPOT_GROUP (member): name[,...]' |
| -W |
| |
--clip |
Apply left and right clips |
| Common Filters. Applied to spots when --split-spot
is not set, otherwise - to individual reads |
| -M |
| |
--minReadLen <len> |
Minimum read length to output, default is 25 |
| -R |
| |
--read-filter <[filter]> |
Split into files by READ_FILTER value optionally filter by
value: pass|reject|criteria|redacted |
| -E |
| |
--qual-filter |
Filter used in early 1000 Genomes data: no sequences starting
or ending with >= 10N |
| Filters based on alignments. Filters are active
when alignment data are present |
|
|
--aligned |
Dump only aligned sequences |
|
|
--unaligned |
Dump only unaligned sequences |
|
|
--aligned-region <name[:from-to]> |
Filter by position on genome. Name can either be
accession.version (ex: NC_000001.10) or file specific name (ex:
'chr1' or '1'). 'from' and 'to' are 1-based coordinates |
|
|
--matepair-distance <from-to|unknown> |
Filter by distance between matepairs. Use 'unknown' to find
matepairs split between the references. Use from-to to limit
matepail distance on the same reference |
| Filters for individual reads. Applied only with
--split-spot set |
|
|
--skip-technical |
Applied only with --split-spot set. Dump only biological
reads |
| Output: |
| -O |
| |
--outdir <path> |
Output directory, default is working directory '.' |
| -Z |
| |
--stdout |
Output to stdout, all split data become joined into single
stream |
|
|
--gzip |
Compress output using gzip |
|
|
--bzip2 |
Compress output using bzip2 |
| Multiple File Options. Setting these options will
produce more than 1 file, each of which will be suffixed according
to splitting criteria |
|
|
--split-files |
Dump each read into separate file. Files will receive suffix
corresponding to read number |
|
|
--split-3 |
Legacy 3-file splitting for mate-pairs: first biological reads
satisfying dumping conditions are placed in files *_1.fastq and
*_2.fastq If only one biological read is present it is placed in
*.fastq. Biological reads and above are ignored |
| -G |
| |
--spot-group |
Split into files by SPOT_GROUP (member name) |
| -R |
| |
--read-filter <[filter]> |
Split into files by READ_FILTER value. Optionally filter by
value: pass|reject|criteria|redacted |
| -T |
| |
--group-in-dirs |
Split into subdirectories instead of files |
| -K |
| |
--keep-empty-files |
Do not delete empty files |
| Formatting: |
| Sequence |
| -C |
| |
--dumpcs <[cskey]> |
Formats sequence using color space (default for SOLiD),'cskey'
may be specified for translation |
| -B |
| |
--dumpbase |
Formats sequence using base space (default for other than
SOLiD) |
| Quality |
| -Q |
| |
--offset <integer> |
Offset to use for quality conversion, default is 33 |
|
|
--fasta <[line width]> |
FASTA only, no qualities, optional line wrap width (set to zero
for no wrapping) |
| Defline |
| -F |
| |
--origfmt |
Defline contains only original sequence name |
| -I |
| |
--readids |
Append read id after spot id as 'accession.spot.readid' on
defline |
|
|
--helicos |
Helicos style defline |
|
|
--defline-seq <fmt> |
Defline format specification for sequence |
|
|
--defline-qual <fmt> |
Defline format specification for quailty. <fmt> is string
of characters and/or variables. The variables can be one of: $ac -
accession, $si spot id, $sn spot name, $sg spot group (barcode),
$sl spot length in bases, $ri read number, $rn read name, $rl read
length in bases. '[]' could be used for an optional output: if all
vars in [] yield empty values whole group is not printed. Empty
value is empty string or for numeric variables. Ex: @$sn[_$rn]/$ri
'_$rn' is omitted if name is empty |
| Other: |
| -h |
| |
--help |
Output brief explanation of program usage |
| -V |
| |
--version |
Display the version of the program |
| -L |
| |
--log-level <level> |
Logging level as number or enum string One of
(fatal|sys|int|err|warn|info) or (0-5). Current/default is
warn |
| -v |
| |
--verbose |
Increase the verbosity level of the program. Use multiple times
for more verbosity |
|
|
--report |
Control program execution environment report generation (if
implemented). One of (never|error|always). Default is error |
