diff --git a/poacns.h b/poacns.h index 9545030..524b3f8 100644 --- a/poacns.h +++ b/poacns.h @@ -89,7 +89,7 @@ typedef struct { float msa_min_freq; } POGPar; -static const POGPar DEFAULT_POG_PAR = (POGPar){0, 0, POG_ALNMODE_OVERLAP, 0, 1, 0, 0, 96, 16, 2, -5, -2, -4, -1, -1.5, 20, 3, 0.5}; +static const POGPar DEFAULT_POG_PAR = (POGPar){0, 0, POG_ALNMODE_OVERLAP, 0, 1, 0, 0, 96, 16, 2, -5, -2, -4, -1, -3, 20, 3, 0.5}; typedef struct { SeqBank *seqs; @@ -857,7 +857,7 @@ static inline int _alignment2graph_pog(POG *g, u4i rid, int xb, int xe){ x = xe; nidx = POG_TAIL_NODE; v = ref_pognodev(g->nodes, nidx); - int my_print = (cns_debug > 2); + int my_print = (cns_debug > 3); if(x + 1 < (int)seqlen){ for(i=seqlen-1;(int)i>x;i--){ if(my_print){ @@ -1088,7 +1088,7 @@ static inline int align_rd_pog(POG *g, u2i rid){ score = POG_SCORE_MIN; mnode = POG_TAIL_NODE; // point to POG_TAIL x = seqlen - 1; - int my_print = (cns_debug > 2); + int my_print = (cns_debug > 3); while(pop_u4v(g->stack, &nidx)){ u = ref_pognodev(g->nodes, nidx); u->rmax = g->rows->buffer[u->roff + seqlex]; @@ -1377,7 +1377,7 @@ static inline u4i realign_msa_pog_core(POG *g, u4i ridx, int W){ } row2[end] = 0; bs[end] = 0; - if(cns_debug > 2){ + if(cns_debug > 3){ fprintf(stderr, "ROW[%u] '%c' %03d-%03d:", i, "ACGT-"[s[i]], beg, end); for(j=beg;j 2 && bt){ + if(cns_debug > 3 && bt){ fprintf(stderr, " -- x = %d y = %d bt = %d in %s -- %s:%d --\n", x, y, bt, __FUNCTION__, __FILE__, __LINE__); fflush(stderr); } } @@ -1737,8 +1737,8 @@ static inline void dp_call_cns_pog(POG *g){ push_u1v(g->cbts, bts[i]); } if(cns_debug > 2){ - fprintf(stderr, "[DPCNS%03u]\t%d\t[%d]\t[%2d, %2d, %2d, %2d, %2d]", col, dep, mx, bcnts[0], bcnts[1], bcnts[2], bcnts[3], bcnts[4]); - fprintf(stderr, "\t[%0.1f, %0.1f, %0.1f, %0.1f, %0.1f]", dp1[0], dp1[1], dp1[2], dp1[3], dp1[4]); + fprintf(stderr, "[DPCNS%03u]\t[%2d, %2d, %2d, %2d, %2d]", col, bcnts[0], bcnts[1], bcnts[2], bcnts[3], bcnts[4]); + //fprintf(stderr, "\t[%0.1f, %0.1f, %0.1f, %0.1f, %0.1f]", dp1[0], dp1[1], dp1[2], dp1[3], dp1[4]); fprintf(stderr, "\t[%0.1f:%d, %0.1f:%d, %0.1f:%d, %0.1f:%d, %0.1f:%d]\n", dp2[0], bts[0], dp2[1], bts[1], dp2[2], bts[2], dp2[3], bts[3], dp2[4], bts[4]); } } diff --git a/wtpoa-cns.c b/wtpoa-cns.c index ef0b400..5715cba 100644 --- a/wtpoa-cns.c +++ b/wtpoa-cns.c @@ -41,7 +41,7 @@ int usage(){ " -X Mismatch score, [-5]\n" " -I Insertion score, [-2]\n" " -D Deletion score, [-4]\n" - " -H Homopolymer merge score used in dp-call-cns mode, [-1.5]\n" + " -H Homopolymer merge score used in dp-call-cns mode, [-3]\n" " -B Bandwidth, [96]\n" " -W Window size in the middle of the first read for fast align remaining reads, [200]\n" " If $W is negative, will disable fast align, but use the abs($W) as Band align score cutoff\n"