Provided by: blasr_0~20151014+git8e668be-1_amd64 
NAME
samtoh5 - convert a SAM file to cmp.h5 format
SYNOPSIS
samtoh5 in.sam reference.fasta out.cmp.h5 [options]
OPTIONS
in.sam Input SAM file.
reference.fasta
Reference used to generate reads.
out.cmp.h5
Output cmp.h5 file.
-smrtTitle
Use this option when converting alignments generated from reads produced by the pls2fasta(1) from
bas.h5 files by parsing read coordinates from the SMRT read title. The title is in the format
/name/hole/coordinates, where coordinates are in the format \d+_\d+, and represent the interval of
the read that was aligned.
-readType value
Set the read type: 'standard', 'strobe', 'CCS', or 'cDNA'
-verbosity value
Set desired verbosity.
-useShortRefName
Use abbreviated reference names obtained from file.sam instead of using full names from
reference.fasta.
-copyQVs
Copy all QVs available in the SAM file into the cmp.h5 file. This includes things like
InsertionQV and DeletionTag.
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 (blasr(1)) it is defined as the start in the query sequence of the alignment. When
-smrtTitle 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.
SEE ALSO
blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtom4(1) sawriter(1) sdpMatcher(1) toAfg(1)