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root/gclib/gclib/GAlnExtend.cpp
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# Line 771 | Line 771
771           if (gx.x(ai,bi))
772             //already have a previous seed covering this region of this diagonal
773             continue;
774 +         //TODO: there could be Ns in this seed, should we count/adjust score?
775           for (int i=0;i<6;i++)
776              gx.x(ai+i,bi+i)=1;
777           //see if we can extend to the right
# Line 864 | Line 865
865    s_alnstart--;
866    if (q_seq==NULL || q_seq[0]==0 || s_seq==NULL || s_seq[0]==0)
867      GError("GreedyAlign() Error: attempt to use an empty sequence string!\n");
868 <  if (q_seq[q_alnstart]!=s_seq[s_alnstart])
869 <    GError("GreedyAlign() Error: improper anchor (mismatch)!\n");
868 >  /*if (q_seq[q_alnstart]!=s_seq[s_alnstart])
869 >    GError("GreedyAlign() Error: improper anchor (mismatch):\n%s (start %d len %d)\n%s (start %d len %d)\n",
870 >           q_seq, q_alnstart, q_max, s_seq, s_alnstart, s_max);
871 >           */
872    int q_ext_l=0, q_ext_r=0, s_ext_l=0, s_ext_r=0;
873    const char* q=q_seq+q_alnstart;
874    int q_avail=q_max-q_alnstart;

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