close unneeded file descriptors

Leaving them open may result in hitting ulimits
on some machines.
clean up memory leaks in GtLTRdigestPdomVisitor
remove stray specialchar
Merge pull request #206 from satta/pdom-fixes

Fixes for GtLTRdigestPdomVisitor
expand gt encseq info
print smallest/largest sequence per file
print N50 per file
touches genometools/genometools#150
expand gt encseq info:
print total n50 values,
option -n50,
print file-details in several lines
touches genometools/genometools#150
create gt encseq sample
extract randomly chosen sequences from an encseq,
output length has to be specified,
all sequences in the encseq must have equal lengths,
touches genometools/genometools#160
cosmetics for gt encseq info:
add prefix gt_encseq_info_ to compare function
add more comments
touches genometools/genometools#150
cosmetics for gt encseq sample:
split output function
shift function calls into runner
touches genometools/genometools#160
gt_free instead of free
Merge pull request #207 from joergi-w/hiwi

expand gt encseq info, create gt encseq sample
remove implicit mapping to first sequence

Accepts the use of '-encseq', '-seqfile' and '-seqfile'
without '-matchdesc' or '-usedesc' only when MD5 tagged
annotations are used.
add gt_strand_invert()
fix strand output in ORF finder
ensure return to silence compiler warnings
Merge pull request #210 from satta/regionmap-options

remove implicit mapping to first sequence
Merge pull request #212 from satta/orf-strand

Fix ORF finder strand output
fix documentation
fix max number of bitshift places for 32 bit
update 32 bit info map