Merge pull request #31 from satta/master

change Sascha Kastens' mail address
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
genometools.h wrapped in #ifdef __cplusplus

allows to include genometools.h into C++ projects
Merge pull request #33 from gordon/master

genometools.h wrapped in #ifdef __cplusplus
fix problem with impossible events in self-trained BSSM

patch by Volker Brendel
Merge pull request #34 from gordon/master

fix problem with impossible events in self-trained BSSM
move static table for byte wise select

refactor determine bits per value
add extern variables to documentation

add module thread to include gt_jobs in the documentation.

closes #37
add static table for byte wise popcount to core/api
Merge pull request #40 from Garonenur/dw

add extern variables to documentation
Implemented GtResetSourceStream class, implemented small functional test with gt gff3
Added D. Standage to contributors
Merge pull request #42 from standage/master

Implemented GtResetSourceStream class
Merge pull request #43 from Garonenur/bytebits

Bytebits
Trying to replace GtResetSourceStream with GtSetSourceVisitor/GtVisitorStream
fix some problems with set source visitor