static const AjPStr assemSAMGetReadgroupHeaderlines(const AjPAssem assem)
{
AjPStr* rgids = NULL;
const AjPAssemReadgroup rg = NULL;
ajint i =0;
ajTableToarrayKeys(assem->Readgroups, (void***)&rgids);
ajStrAssignC(&assemoutSamLinetxt, "");
while (rgids[i]) /* read groups */
{
rg = ajTableFetchS(assem->Readgroups, rgids[i++]);
ajFmtPrintAppS(&assemoutSamLinetxt, "@RG\tID:%S", rg->ID);
if(rg->CN)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tCN:%S", rg->CN);
if(rg->Desc)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tDS:%S", rg->Desc);
if(rg->Date)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tDT:%S", rg->Date);
if(rg->FlowOrder)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tFO:%S", rg->FlowOrder);
if(rg->KeySeq)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tKS:%S", rg->KeySeq);
if(rg->Library)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tLB:%S", rg->Library);
if(rg->Programs)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tPG:%S", rg->Programs);
if(rg->Isize)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tPI:%d", rg->Isize);
if(rg->Platform)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tPL:%s",
ajAssemreadgroupGetPlatformname(rg));
if(rg->Unit)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tPU:%S", rg->Unit);
if(rg->Sample)
ajFmtPrintAppS(&assemoutSamLinetxt, "\tSM:%S", rg->Sample);
ajStrAppendC(&assemoutSamLinetxt, "\n");
}
AJFREE(rgids);
return assemoutSamLinetxt;
}
static void remap_CutList(AjPFile outfile, const AjPTable hittable,
AjBool isos,
AjBool html, ajint mincuts, ajint maxcuts)
{
const PValue value;
void **keyarray = NULL; /* array for table */
ajint i;
/* print title */
if(html)
ajFmtPrintF(outfile, "<H2>");
ajFmtPrintF(outfile, "\n\n# Enzymes that cut Frequency");
if(isos)
ajFmtPrintF(outfile, "\tIsoschizomers\n");
else
ajFmtPrintF(outfile, "\n");
if(html)
ajFmtPrintF(outfile, "</H2>\n");
if(ajTableGetLength(hittable))
{
ajTableToarrayKeys(hittable, &keyarray);
qsort(keyarray, ajTableGetLength(hittable), sizeof (*keyarray),
ajStrVcmp);
/* enzymes that cut the required number of times */
if(html)
ajFmtPrintF(outfile, "<PRE>");
for(i = 0; keyarray[i]; i++)
{
value = ajTableFetchS(hittable,keyarray[i]);
if(value->count >= mincuts && value->count <= maxcuts)
ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
(AjPStr) keyarray[i], value->count,
value->iso);
}
ajFmtPrintF(outfile, "\n");
if(html)
ajFmtPrintF(outfile, "</PRE>\n");
}
/* enzymes that cut <mincuts */
/* print title */
if(html)
ajFmtPrintF(outfile, "<H2>");
ajFmtPrintF(outfile, "\n\n# Enzymes which cut less frequently than the ");
ajFmtPrintF(outfile, "MINCUTS criterion\n# Enzymes < MINCUTS Frequency");
if(isos)
ajFmtPrintF(outfile, "\tIsoschizomers\n");
else
ajFmtPrintF(outfile, "\n");
if(html)
ajFmtPrintF(outfile, "</H2>\n");
if(ajTableGetLength(hittable))
{
/* print out results */
if(html)
ajFmtPrintF(outfile, "<PRE>");
for(i = 0; keyarray[i]; i++)
{
value = ajTableFetchS(hittable,keyarray[i]);
if(value->count < mincuts)
ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
(AjPStr) keyarray[i], value->count,
value->iso);
}
ajFmtPrintF(outfile, "\n");
if(html)
ajFmtPrintF(outfile, "</PRE>\n");
}
/* enzymes that cut >maxcuts */
/* print title */
if(html)
ajFmtPrintF(outfile, "<H2>");
ajFmtPrintF(outfile, "\n\n# Enzymes which cut more frequently than the ");
ajFmtPrintF(outfile, "MAXCUTS criterion\n# Enzymes > MAXCUTS Frequency");
if(isos)
ajFmtPrintF(outfile, "\tIsoschizomers\n");
else
ajFmtPrintF(outfile, "\n");
if(html)
ajFmtPrintF(outfile, "</H2>\n");
if(ajTableGetLength(hittable))
{
/* print out results */
if(html)
ajFmtPrintF(outfile, "<PRE>");
for(i = 0; keyarray[i]; i++)
{
value = ajTableFetchS(hittable,keyarray[i]);
if(value->count > maxcuts)
ajFmtPrintF(outfile, "%10S\t %d\t%S\n",
(AjPStr) keyarray[i], value->count,
value->iso);
}
ajFmtPrintF(outfile, "\n");
if(html)
ajFmtPrintF(outfile, "</PRE>\n");
AJFREE(keyarray);
}
return;
}
