.TH SAMTOH5 "1" "July 2015" "samtoh5 3ca7fe8" "User Commands"
.SH NAME
samtoh5 \- convert a SAM file to cmp.h5 format
.SH SYNOPSIS
.B samtoh5 
.I in.sam
.I reference.fasta
.I out.cmp.h5
.RI [ options ]
.SH OPTIONS
.TP
.I in.sam
Input SAM file.
.TP
.I reference.fasta
Reference used to generate reads.
.TP
.I out.cmp.h5
Output cmp.h5 file.
.TP
.B \-smrtTitle
Use this option when converting alignments generated from reads
produced by the
.BR pls2fasta (1)
from bas.h5 files by parsing read
coordinates from the SMRT read title. The title is in the
format \fI\,/name/hole/coordinates\/\fP, where coordinates are in the
format \ed+_\ed+, and represent the interval of the read that was
aligned.
.TP
.BI \-readType \0value
Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'
.TP
.BI \-verbosity \0value
Set desired verbosity.
.TP
.B \-useShortRefName
Use abbreviated reference names obtained from \fIfile.sam\fR instead
of using full names from \fIreference.fasta\fR.
.TP
.B \-copyQVs
Copy all QVs available in the SAM file into the cmp.h5 file.
This includes things like InsertionQV and DeletionTag.
.SH NOTES
Because SAM has optional tags that have different meanings in different
programs, careful usage is required in order to have proper output. The
"xs" tag in bwa\-sw is used to show the suboptimal score, but in PacBio SAM
.RB ( blasr (1))
it is defined as the start in the query sequence of the alignment.
When \fB\-smrtTitle\fR is specified, the xs tag is ignored, but when it is not
specified, the coordinates given by the xs and xe tags are used to define
the interval of a read that is aligned. The CIGAR string is relative to
this interval.
.SH SEE ALSO
.BR blasr (1)
.BR loadPulses (1)
.BR pls2fasta (1)
.BR samFilter (1)
.BR samtom4 (1)
.BR sawriter (1)
.BR sdpMatcher (1)
.BR toAfg (1)