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.