add gt_tir_stream_get_encseq()
add gt_ltrdigest_pdom_visitor_set_{root_type,source_tag}()
fix bug in GtLTRdigestPdomVisitor

some pHMMs contain consensus annotation -- in this case
there is an additional line in the output which must be taken
into account
extend `gt tirvish' tool with pHMM search

This commit adds profile HMM search to the TIRvish tool,
much similar to the implementation in the LTRdigest tool.
It allows for the detection of internal transposase (e.g.
DDE) domains inside de novo detected candidates.
Merge pull request #32 from satta/tir_pdom

add pHMM protein domain search to TIRvish