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)