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chore: Add old cli-output
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edmundmiller committed Dec 22, 2023
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```
dragenos -r <reference> -b <base calls> [optional arguments]
Command line options:
--Aligner.pe-orientation arg Expected paired-end
orientation: 0=FR, 1=RF, 2=FF
--Aligner.pe-stat-mean-insert arg (=0) Expected mean of the insert
size
--Aligner.pe-stat-mean-read-len arg (=0) When setting paired-end
insert stats, the expected
mean read length
--Aligner.pe-stat-quartiles-insert arg Q25, Q50, and Q75 quartiles
for the insert size
--Aligner.pe-stat-stddev-insert arg (=0) Expected standard deviation
of the insert size
--Aligner.rescue-ceil-factor arg (=3) For tuning the rescue scan
window maximum ceiling
--Aligner.rescue-sigmas arg (=0) For tuning the rescue scan
window
--Aligner.sec-aligns arg (=0) Maximum secondary
(suboptimal) alignments to
report per read
--Aligner.sec-aligns-hard arg (=0) Set to force unmapped when
not all secondary alignments
can be output
--Aligner.sec-phred-delta arg (=0) Only secondary alignments
with likelihood within this
phred of the primary
--Aligner.sec-score-delta arg (=0) Secondary aligns allowed with
pair score no more than this
far below primary
--Aligner.smith-waterman-method arg Smith Waterman implementation
(dragen / mengyao default =
dragen)
--Aligner.sw-all arg (=0) Value of 1 forces smith
waterman on all candidate
alignments
--Mapper.filter-len-ratio arg (=4) Ratio for controlling seed
chain filtering
--RGID arg (=1) Read Group ID
--RGSM arg (=none) Read Group Sample
-b [ --bam-input ] arg Input BAM file
--build-hash-table arg (=0) Generate a reference/hash
table
--enable-sampling arg (=1) Automatically detect
paired-end parameters by
running a sample through the
mapper/aligner
-1 [ --fastq-file1 ] arg FASTQ file to send to card
(may be gzipped)
-2 [ --fastq-file2 ] arg Second FASTQ file with
paired-end reads (may be
gzipped)
--fastq-offset arg (=33) FASTQ quality offset value.
Set to 33 or 64
-h [ --help ] produce help message and exit
--help-defaults produce tab-delimited list of
command line options and
their default values
--ht-anchor-bin-bits arg (=0) Bits defining reference bins
for anchored seed search
--ht-cost-coeff-seed-freq arg (=0.5) Cost coefficient of extended
seed frequency
--ht-cost-coeff-seed-len arg (=1) Cost coefficient of extended
seed length
--ht-cost-penalty arg (=0) Cost penalty to extend a seed
by any number of bases
--ht-cost-penalty-incr arg (=0.69999999999999996)
Cost penalty to incrementally
extend a seed another step
--ht-crc-extended arg (=0) Index of CRC polynomial for
hashing extended seeds
--ht-crc-primary arg (=0) Index of CRC polynomial for
hashing primary seeds
--ht-decoys arg Path to decoys file (FASTA
format)
--ht-dump-int-params arg (=0) Testing - dump internal
parameters
--ht-ext-rec-cost arg (=4) Cost penalty for each EXTEND
or INTERVAL record
--ht-ext-table-alloc arg (=0) 8-byte records to reserve in
extend_table.bin
(0=automatic)
--ht-mask-bed arg Bed file for base masking
--ht-max-dec-factor arg (=1) Maximum decimation factor for
seed thinning
--ht-max-ext-incr arg (=12) Maximum bases to extend a
seed by in one step
--ht-max-ext-seed-len arg (=0) Maximum extended seed length
--ht-max-multi-base-seeds arg Maximum seeds populated at
multi-base codes
--ht-max-seed-freq arg (=16) Maximum allowed frequency for
a seed match after extension
attempts
--ht-max-seed-freq-len arg (=98) Ramp from priMaxSeedFreq
reaches maxSeedFreq at this
seed length
--ht-max-table-chunks arg Maximum ~1GB thread table
chunks in memory at once
--ht-mem-limit arg (=0GB) Memory limit (hash table +
reference)
--ht-methylated arg (=0) If set to true, generate C->T
and G->A converted pair of
hashtables
--ht-min-repair-prob arg (=0.20000000000000001) Minimum probability of
success to attempt extended
seed repair
--ht-num-threads arg Worker threads for generating
hash table
--ht-override-size-check arg (=0) Override hash table size
check
--ht-pri-max-seed-freq arg (=0) Maximum frequency for a
primary seed match (0 => use
maxSeedFreq)
--ht-rand-hit-extend arg (=8) Include a random hit with
each EXTEND record of this
frequency
--ht-rand-hit-hifreq arg (=1) Include a random hit with
each HIFREQ record
--ht-ref-seed-interval arg Number of positions per
reference seed
--ht-reference arg Reference in FASTA format
--ht-repair-strategy arg (=0) Seed extension repair
strategy: 0=none, 1=best,
2=rand
--ht-seed-len arg (=21) Initial seed length to store
in hash table
--ht-size arg (=0GB) Size of hash table, units
B|KB|MB|GB
--ht-sj-size arg Reserved space for RNA
annotated SJs, units
B|KB|MB|GB
--ht-soft-seed-freq-cap arg (=12) Soft seed frequency cap for
thinning
--ht-target-seed-freq arg (=4) Target seed frequency for
seed extension
--ht-test-only arg (=0) Testing - show user
parameters, but don't do
anything
--ht-uncompress arg (=0) Uncompress hash_table.cmp to
hash_table.bin and
extend_table.bin (standalone
option)
--ht-write-hash-bin arg (=0) Write decompressed
hash_table.bin and
extend_table.bin (0/1)
--input-qname-suffix-delimiter arg (= ) Character that delimits input
qname suffixes, e.g. / for /1
--interleaved [=arg(=1)] (=0) Interleaved paired-end reads
in single bam or FASTQ
--map-only arg (=0) no real alignment, produces
alignment information based
on seed chains only
--mmap-reference arg (=0) memory-map reference data
instead of pre-loading. This
allows for quicker runs when
only a handful of reads need
to be aligned
--num-threads arg (=16) Worker threads for
mapper/aligner (default =
maximum available on system)
--output-directory arg Output directory
--output-file-prefix arg Output filename prefix
--pe-stats-interval-delay arg (=) Number of intervals of lag
between sending reads and
using resulting stats
--pe-stats-interval-memory arg (=
) Include reads from up to this
many stats intervals in
paired-end stats calculations
--pe-stats-interval-size arg (=25000) Number of reads to include in
each interval of updating
paired-end stats
--pe-stats-sample-size arg (=100000) Number of most recent pairs
to include in each update of
the paired-end stats
--preserve-map-align-order arg (=0) Preserve the order of
mapper/aligner output to
produce deterministic
results. Impacts performance
-r [ --ref-dir ] arg directory with reference and
hash tables. Must contain the
uncompressed hashtable.
--ref-load-hash-bin arg (=0) Expect to find uncompressed
hash table in the reference
directory.
--response-file arg file with more command line
arguments
-v [ --verbose ] Be talkative
-V [ --version ] print program version
information
Failed to parse the options: /build/i5zj4f8yjlk2spizc3krc2x4k1yqkvz1-source/src/lib/options/DragenOsOptions.cpp(335): Throw in function postProcess
Dynamic exception type: boost::wrapexcept<dragenos::common::InvalidOptionException>
std::exception::what: fastq-file1 or bam-input must point to an existing fastq file
```

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