static void showcomparisonfailure(const char *filename,
int line,
const char *where,
const GtEncseq *encseq,
GtReadmode readmode,
const GtSuffixsortspace *suffixsortspace,
GtUword subbucketleft,
GtUword depth,
GtUword idx1,
GtUword idx2,
int cmp,
GtUword maxlcp)
{
GtUword pos1, pos2;
pos1 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx1);
pos2 = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx2);
fprintf(stderr,"ERROR: file \"%s\", line %d: ",filename,line);
fprintf(stderr,"%s("GT_WU" vs "GT_WU""
" "GT_WU"=\"",
where,
idx1,
idx2,
pos1);
gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,pos1,depth);
fprintf(stderr,"\",\"");
gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,pos2,depth);
fprintf(stderr,"\"="GT_WU")=%d with maxlcp "GT_WU",depth="GT_WU"\n",pos2,cmp,
maxlcp,depth);
}
void gt_Outlcpinfo_check_lcpvalues(const GtEncseq *encseq,
GtReadmode readmode,
const GtSuffixsortspace *sortedsample,
GtUword effectivesamplesize,
const GtOutlcpinfo *outlcpinfosample,
bool checkequality)
{
GT_UNUSED int cmp;
GtUword idx, reallcp, startpos1, startpos2, currentlcp,
totalcmpmissing = 0;
if (effectivesamplesize == 0)
{
return;
}
startpos1 = gt_suffixsortspace_getdirect(sortedsample,0);
for (idx=1UL; idx<effectivesamplesize; idx++)
{
startpos2 = gt_suffixsortspace_getdirect(sortedsample,idx);
cmp = gt_encseq_check_comparetwosuffixes(encseq,
readmode,
&reallcp,
false,
false,
0,
startpos1,
startpos2,
NULL,
NULL);
gt_assert(cmp <= 0);
gt_assert(GT_ISIBITSET(outlcpinfosample->lcpsubtab.tableoflcpvalues
.isset,idx));
currentlcp = (GtUword) outlcpinfosample->lcpsubtab.tableoflcpvalues.
bucketoflcpvalues[idx];
if ((checkequality && currentlcp != reallcp) ||
(!checkequality && currentlcp > reallcp))
{
fprintf(stderr,"idx="GT_WU",suffixpair="GT_WU","GT_WU": "
"currentlcp = "GT_WU" %s "GT_WU" = reallcp\n",
idx,startpos1,startpos2,currentlcp,
checkequality ? "!=" : ">",reallcp);
gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,startpos1,50UL);
fprintf(stderr,"\n");
gt_encseq_showatstartposwithdepth(stderr,encseq,readmode,startpos2,50UL);
fprintf(stderr,"\n");
exit(GT_EXIT_PROGRAMMING_ERROR);
} else
{
totalcmpmissing += (reallcp - currentlcp);
}
startpos1 = startpos2;
}
/*printf("totalcmpmissing = "GT_WU"(avg=%.2f)\n",
totalcmpmissing,(double) totalcmpmissing/effectivesamplesize);*/
}
static int processleafedge_shulen(bool firstsucc,
unsigned long fatherdepth,
GtBUinfo_shulen *father,
unsigned long leafnumber,
GtBUstate_shulen *state,
GT_UNUSED GtError *err)
{
unsigned long gnum;
#ifdef SHUDEBUG
printf("processleafedge %lu firstsucc=%s, "
" depth(father)=%lu, path=",
leafnumber,
firstsucc ? "true" : "false",
fatherdepth);
if (fatherdepth > 0)
{
gt_encseq_showatstartposwithdepth(stdout,
state->encseq,
GT_READMODE_FORWARD,
leafnumber,
fatherdepth);
}
printf("\n");
#endif
if (state->file_to_genome_map != NULL)
{
gnum = state->file_to_genome_map[gt_encseq_filenum(state->encseq,
leafnumber)];
} else
{
gnum = gt_encseq_filenum(state->encseq,leafnumber);
}
if (firstsucc)
{
gt_assert(father != NULL);
if (father->gnumdist == NULL)
{
father->gnumdist
= gt_malloc(sizeof (*father->gnumdist) * state->numofdbfiles);
}
resetgnumdist_shulen(father,state->numofdbfiles);
#ifdef SHUDEBUG
shownode(__LINE__,state,"father",father);
#endif
} else
{
#ifdef SHUDEBUG
shownode(__LINE__,state,"father",father);
#endif
shu_compute_leaf_edge_contrib(state,father->gnumdist,gnum,fatherdepth);
}
father->gnumdist[gnum]++;
#ifdef SHUDEBUG
printf("gnumdist[id=%lu,filenum=%lu]=%lu\n",father->id,gnum,
father->gnumdist[gnum]);
state->lastleafnumber = leafnumber;
#endif
return 0;
}
void gt_showentiresuftab(const GtEncseq *encseq,
GtReadmode readmode,
const GtSuffixsortspace *suffixsortspace,
GtUword subbucketleft,
GtUword depth)
{
GtUword idx, pos, totallength = gt_encseq_total_length(encseq);
for (idx = 0; idx <= totallength; idx++)
{
pos = gt_suffixsortspace_get(suffixsortspace,subbucketleft,idx);
printf("suftab["GT_WU"]="GT_WU" ",idx,pos);
gt_encseq_showatstartposwithdepth(stdout,encseq,readmode,pos,depth);
printf("\n");
}
}
static int processbranchingedge_shulen(bool firstsucc,
unsigned long fatherdepth,
GtBUinfo_shulen *father,
GT_UNUSED unsigned long sondepth,
GT_UNUSED unsigned long sonwidth,
GtBUinfo_shulen *son,
GtBUstate_shulen *state,
GT_UNUSED GtError *err)
{
unsigned long idx;
#ifdef SHUDEBUG
printf("%s firstsucc=%s, depth(father)=%lu,path=",__func__,
firstsucc ? "true" : "false",fatherdepth);
if (fatherdepth > 0)
{
gt_encseq_showatstartposwithdepth(stdout,
state->encseq,
GT_READMODE_FORWARD,
state->lastleafnumber,
fatherdepth);
}
printf("\n");
#endif
if (firstsucc)
{
gt_assert(father != NULL);
if (father->gnumdist == NULL)
{
father->gnumdist
= gt_malloc(sizeof (*father->gnumdist) * state->numofdbfiles);
resetgnumdist_shulen(father,state->numofdbfiles);
}
#ifdef SHUDEBUG
shownode(__LINE__,state,"father",father);
#endif
} else
{
#ifdef SHUDEBUG
gt_assert(father != NULL);
shownode(__LINE__,state,"father",father);
gt_assert(son != NULL);
shownode(__LINE__,state,"son",son);
#endif
cartproduct_shulen(state, fatherdepth, father->gnumdist, son->gnumdist);
cartproduct_shulen(state, fatherdepth, son->gnumdist, father->gnumdist);
}
if (son != NULL)
{
for (idx = 0; idx < state->numofdbfiles; idx++)
{
father->gnumdist[idx] += son->gnumdist[idx];
son->gnumdist[idx] = 0;
#ifdef SHUDEBUG
printf("gnumdist[id=%lu,filenum=%lu]=%lu\n",father->id,idx,
father->gnumdist[idx]);
printf("gnumdist[id=%lu,filenum=%lu]=0\n",son->id,idx);
#endif
}
}
return 0;
}