[FEATURE] Adding --ignore-paired-flags flag to rabema_evaluate
[FEATURE] Adding --ignore-paired-flags flag to rabema_evaluate

Using this flag makes RABEMA ignore the pairedness flags.  This is required for evaluating the SAM output of soap2sam.pl since the latter sets the flags incorrectly.


git-svn-id: a7f2a8f7432d210e972fb03898013d213e2b549b@13777 e6417c60-b987-48fd-844e-b20f0fcc1017

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