[FIX] Fixing seqcons input bug.
[FIX] Fixing seqcons input bug.

There was a problem with the loading of FASTA files where even single-ended reads were assigned a mate id.
This caused problems when writing as SAM.


git-svn-id: a7f2a8f7432d210e972fb03898013d213e2b549b@13891 e6417c60-b987-48fd-844e-b20f0fcc1017

PF2-pasteur-fr/seqan,ktrappe/seqan,xp3i4/seqan,limeng12/seqan,bayolau/seqan,catkira/seqan,xenigmax/seqan,catkira/seqan,xenigmax/seqan,weese/seqan,h-2/seqan,h-2/seqan,holtgrewe/seqan,bestrauc/seqan,holtgrewe/seqan,catkira/seqan,h-2/seqan,hannespetur/SeqAnHTS,bestrauc/seqan,PF2-pasteur-fr/seqan,budach/seqan,ktrappe/seqan,weese/seqan,weese/seqan,PF2-pasteur-fr/seqan,h-2/seqan,hannespetur/SeqAnHTS,holtgrewe/seqan,JohnReid/seqan,xenigmax/seqan,ktrappe/seqan,budach/seqan,catkira/seqan,xenigmax/seqan,bayolau/seqan,PF2-pasteur-fr/seqan,catkira/seqan,budach/seqan,ktrappe/seqan,PF2-pasteur-fr/seqan,JohnReid/seqan,PF2-pasteur-fr/seqan,h-2/seqan,ktrappe/seqan,limeng12/seqan,JohnReid/seqan,holtgrewe/seqan,holtgrewe/seqan,xp3i4/seqan,h-2/seqan,xp3i4/seqan,weese/seqan,weese/seqan,xp3i4/seqan,JohnReid/seqan,hannespetur/SeqAnHTS,catkira/seqan,h-2/seqan,bayolau/seqan,budach/seqan,limeng12/seqan,bayolau/seqan,xenigmax/seqan,limeng12/seqan,PF2-pasteur-fr/seqan,hannespetur/SeqAnHTS,xp3i4/seqan,xp3i4/seqan,bestrauc/seqan,hannespetur/SeqAnHTS,ktrappe/seqan,JohnReid/seqan,hannespetur/SeqAnHTS,budach/seqan,ktrappe/seqan,xenigmax/seqan,budach/seqan,JohnReid/seqan,limeng12/seqan,catkira/seqan,bestrauc/seqan,hannespetur/SeqAnHTS,weese/seqan,bayolau/seqan,catkira/seqan,budach/seqan,bayolau/seqan,bestrauc/seqan,bayolau/seqan,xp3i4/seqan,ktrappe/seqan,budach/seqan,budach/seqan,xenigmax/seqan,bestrauc/seqan,holtgrewe/seqan,JohnReid/seqan,JohnReid/seqan,bayolau/seqan,bestrauc/seqan,holtgrewe/seqan,hannespetur/SeqAnHTS,ktrappe/seqan,xp3i4/seqan,xenigmax/seqan,catkira/seqan,weese/seqan,limeng12/seqan,h-2/seqan,hannespetur/SeqAnHTS,bestrauc/seqan,limeng12/seqan,weese/seqan,PF2-pasteur-fr/seqan,limeng12/seqan,PF2-pasteur-fr/seqan,h-2/seqan,bayolau/seqan,JohnReid/seqan,holtgrewe/seqan,xp3i4/seqan,limeng12/seqan