void print_maf_job_header
(FILE* f,
char* _programName,
char* _args,
scoreset* scoring,
sthresh* hspThreshold,
sthresh* gappedThreshold,
score xDrop,
score yDrop,
int withComments)
{
char* programName = _programName;
char* args = _args;
if (!withComments) return;
if (programName == NULL) programName = "(no name)";
if (args == NULL) args = "";
fprintf (f, "##maf version=1 scoring=%s\n", programName);
fprintf (f, "# %s %s\n", programName, args);
fprintf (f, "#\n");
fprintf (f, "# hsp_threshold = %s\n", score_thresh_to_string (hspThreshold));
if ((gappedThreshold->t == 'S') || (hspThreshold->t == 'S'))
fprintf (f, "# gapped_threshold = %s\n", score_thresh_to_string (gappedThreshold));
else
fprintf (f, "# gapped_threshold = (derived from hsp_threshold)\n");
fprintf (f, "# x_drop = " scoreFmtSimple "\n", xDrop);
fprintf (f, "# y_drop = " scoreFmtSimple "\n", yDrop);
print_score_matrix_prefix (f, scoring, true, "# ");
}
void print_lav_job_header
(FILE* f,
char* _programName,
char* _name1,
char* _name2,
char* _args,
scoreset* scoring,
sthresh* hspThreshold,
sthresh* gappedThreshold,
u8 dynamicMasking)
{
char* programName = _programName;
char* name1 = _name1;
char* name2 = _name2;
char* args = _args;
if (programName == NULL) programName = "(no name)";
if (name1 == NULL) name1 = "(no name)";
if (name2 == NULL) name2 = "(no name)";
if (args == NULL) args = "";
fprintf (f, "#:lav\n");
fprintf (f, "d {\n");
fprintf (f, " \"%s %s %s %s\n", programName, name1, name2, args);
print_score_matrix (f, scoring, false);
fprintf (f, " O = " scoreFmtSimple
", E = " scoreFmtSimple
", K = %s"
", L = %s"
", M = %d\"\n",
scoring->gapOpen, scoring->gapExtend,
score_thresh_to_string (hspThreshold),
score_thresh_to_string (gappedThreshold),
dynamicMasking);
fprintf (f, "}\n");
}
