.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH PBALIGN "1" "December 2015" "pbalign 0.2.0" "User Commands"
.SH NAME
pbalign \- Mapping PacBio sequences to references
.SH DESCRIPTION
usage: pbalign [\-h] [\-\-verbose] [\-\-version] [\-\-profile] [\-\-debug]
.IP
[\-\-regionTable REGIONTABLE] [\-\-configFile CONFIGFILE]
[\-\-pulseFile PULSEFILE] [\-\-algorithm {blasr,bowtie,gmap}]
[\-\-maxHits MAXHITS] [\-\-minAnchorSize MINANCHORSIZE]
[\-\-useccs {useccs,useccsall,useccsdenovo}] [\-\-noSplitSubreads]
[\-\-concordant] [\-\-nproc NPROC]
[\-\-algorithmOptions ALGORITHMOPTIONS]
[\-\-maxDivergence MAXDIVERGENCE] [\-\-minAccuracy MINACCURACY]
[\-\-minLength MINLENGTH]
[\-\-scoreFunction {alignerscore,editdist,blasrscore}]
[\-\-scoreCutoff SCORECUTOFF]
[\-\-hitPolicy {randombest,allbest,random,all,leftmost}]
[\-\-filterAdapterOnly] [\-\-forQuiver] [\-\-loadQVs] [\-\-byread]
[\-\-metrics METRICS] [\-\-seed SEED] [\-\-tmpDir TMPDIR]
inputFileName referencePath outputFileName
.PP
Mapping PacBio sequences to references using an algorithm
selected from a selection of supported command\-line alignment
algorithms. Input can be a fasta, pls.h5, bas.h5 or ccs.h5
file or a fofn (file of file names). Output is in either
cmp.h5 or sam format.
.SS "positional arguments:"
.TP
inputFileName
The input file can be a fasta, plx.h5, bax.h5, ccs.h5
file or a fofn.
.TP
referencePath
Either a reference fasta file or a reference repository.
.TP
outputFileName
The output cmp.h5 or sam file.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-verbose\fR, \fB\-v\fR
Set the verbosity level
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-\-profile\fR
Print runtime profile at exit
.TP
\fB\-\-debug\fR
Catch exceptions in debugger (requires ipdb)
.TP
\fB\-\-regionTable\fR REGIONTABLE
Specify a region table for filtering reads.
.TP
\fB\-\-configFile\fR CONFIGFILE
Specify a set of user\-defined argument values.
.TP
\fB\-\-pulseFile\fR PULSEFILE
When input reads are in fasta format and output is a cmp.h5
this option can specify pls.h5 or bas.h5 or
FOFN files from which pulse metrics can be loaded for Quiver.
.TP
\fB\-\-algorithm\fR {blasr,bowtie,gmap}
Select an aligorithm from ('blasr', 'bowtie', 'gmap').
Default algorithm is blasr.
.TP
\fB\-\-maxHits\fR MAXHITS
The maximum number of matches of each read to the
reference sequence that will be evaluated. Default
value is 10.
.TP
\fB\-\-minAnchorSize\fR MINANCHORSIZE
The minimum anchor size defines the length of the read
that must match against the reference sequence. Default
value is 12.
.TP
\fB\-\-useccs\fR {useccs,useccsall,useccsdenovo}
Map the ccsSequence to the genome first, then align
subreads to the interval that the CCS reads mapped to.
.TP
useccs: only maps subreads that span the length of
the template.
.TP
useccsall: maps all subreads.
useccsdenovo: maps ccs only.
.TP
\fB\-\-noSplitSubreads\fR
Do not split reads into subreads even if subread
regions are available. Default value is False.
.TP
\fB\-\-concordant\fR
Map subreads of a ZMW to the same genomic location.
.TP
\fB\-\-nproc\fR NPROC
Number of threads. Default value is 8.
.TP
\fB\-\-algorithmOptions\fR ALGORITHMOPTIONS
Pass alignment options through.
.TP
\fB\-\-maxDivergence\fR MAXDIVERGENCE
The maximum allowed percentage divergence of a read
from the reference sequence. Default value is 30.
.TP
\fB\-\-minAccuracy\fR MINACCURACY
The minimum percentage accuracy of alignments that
will be evaluated. Default value is 70.
.TP
\fB\-\-minLength\fR MINLENGTH
The minimum aligned read length of alignments that
will be evaluated. Default value is 50.
.TP
\fB\-\-scoreFunction\fR {alignerscore,editdist,blasrscore}
Specify a score function for evaluating alignments.
.TP
alignerscore : aligner's score in the SAM tag 'as'.
editdist     : edit distance between read and reference.
blasrscore   : blasr's default score function.
.IP
Default value is alignerscore.
.TP
\fB\-\-scoreCutoff\fR SCORECUTOFF
The worst score to output an alignment.
.TP
\fB\-\-hitPolicy\fR {randombest,allbest,random,all,leftmost}
Specify a policy for how to treat multiple hit
.TP
random
: selects a random hit.
.TP
all
: selects all hits.
.TP
allbest
: selects all the best score hits.
.TP
randombest: selects a random hit from all best score hits.
leftmost  : selects a hit which has the best score and the
.TP
smallest mapping coordinate in any reference.
Default value is randombest.
.TP
\fB\-\-filterAdapterOnly\fR
If specified, do not report adapter\-only hits using
annotations with the reference entry.
.TP
\fB\-\-forQuiver\fR
The output cmp.h5 file which will be sorted, loaded
with pulse QV information, and repacked, so that it
can be consumed by quiver directly. This requires
the input file to be in PacBio bas/pls.h5 format,
and \fB\-\-useccs\fR must be None. Default value is False.
.TP
\fB\-\-loadQVs\fR
Similar to \fB\-\-forQuiver\fR, the only difference is that
\fB\-\-useccs\fR can be specified. Default value is False.
.TP
\fB\-\-byread\fR
Load pulse information using \fB\-byread\fR option instead
of \fB\-bymetric\fR. Only works when \fB\-\-forQuiver\fR or
\fB\-\-loadQVs\fR are set. Default value is False.
.TP
\fB\-\-metrics\fR METRICS
Load the specified (comma\-delimited list of) metrics
instead of the default metrics required by quiver.
This option only works when \fB\-\-forQuiver\fR  or
\fB\-\-loadQVs\fR are set. Default: DeletionQV,DeletionTag,InsertionQV,MergeQV,SubstitutionQV
.TP
\fB\-\-seed\fR SEED
Initialize the random number generator with a none\-zero
integer. Zero means that current system time is used.
Default value is 1.
.TP
\fB\-\-tmpDir\fR TMPDIR
Specify a directory for saving temporary files.
Default is \fI\,/scratch\/\fP.