void print_leftovers(Read const &read, const char * tag, std::ostream *LEFTOVER_FP)
{
_stats.alignment_num_unmapped++ ;
if (read.get_orig()==NULL)
{
if (read.format() == 0)
fprintf(LEFTOVER_FP, "@%s%s\n%s\n+\n%s\n", read.id(), tag, read.data(), read.quality(0));
else if (read.format() == 1)
fprintf(LEFTOVER_FP, ">%s%s\n%s\n", read.id(), tag, read.data());
else {
fprintf(LEFTOVER_FP, "%s%s\t%s\t%d", read.id(), tag, read.data(), read.pe_flag());
if (strlen(read.quality(0)) > 0) fprintf(LEFTOVER_FP, "\t%s", read.quality(0));
if (strlen(read.quality(1)) > 0) fprintf(LEFTOVER_FP, "\t%s", read.quality(1));
if (strlen(read.quality(2)) > 0) fprintf(LEFTOVER_FP, "\t%s", read.quality(2));
fprintf(LEFTOVER_FP, "\n");
}
}
else
{
if (read.format() == 0)
fprintf(LEFTOVER_FP, "@%s%s\n%s\n+\n%s\n", read.id(), tag, read.get_orig()->data(), read.get_orig()->quality(0));
else if (read.format() == 1)
fprintf(LEFTOVER_FP, ">%s%s\n%s\n", read.id(), tag, read.get_orig()->data());
else {
fprintf(LEFTOVER_FP, "%s%s\t%s\t%d", read.id(), tag, read.get_orig()->data(), read.pe_flag());
if (strlen(read.get_orig()->quality(0)) > 0) fprintf(LEFTOVER_FP, "\t%s", read.get_orig()->quality(0));
if (strlen(read.get_orig()->quality(1)) > 0) fprintf(LEFTOVER_FP, "\t%s", read.get_orig()->quality(1));
if (strlen(read.get_orig()->quality(2)) > 0) fprintf(LEFTOVER_FP, "\t%s", read.get_orig()->quality(2));
fprintf(LEFTOVER_FP, "\n");
}
}
}
void print_alignment_matrix(Read const &read, int chrstart, int readstart, int length,
int offset_front, int offset_end, Chromosome const &chr, char ori, int K) {
int i, j;
printf(" k=%d |\t-\t", K);
if (ori == '+')
for (i = 0; i != length; i++)
printf("%c\t", chr[chrstart + i]);
else
for (i = 0; i != length; i++)
printf("%c\t", get_compl_base(chr[chrstart - i]));
printf(
"\n----------------------------------------------------------------------------------------------");
printf(
"----------------------------------------------------------------------------------------------\n");
for (j = 0; j != length + 1; ++j) {
if (j == 0)
printf(" - |\t");
else {
if ((readstart == 0 && (j <= offset_front || (j > length
- offset_end && K != 1))) || (readstart != 0 && j > length
- offset_end))
printf(" X |\t");
else
printf(" %c |\t", read.data()[readstart + j - (readstart == 0)
* offset_front - 1]);
}
if (j > K)
for (i = 0; i != j - K; ++i)
printf("\t");
for (i = 0; i != 2* K + 1; ++i) {
if (i - j > K)
break;
if (i + j > length + K)
break;
if (i > length || j > length)
break;
if ((readstart != 0 && j > length - offset_end) || (readstart == 0
&& j < offset_front))
break;
//printf("{i%d,j%d}",i,j);
//printf("%.1f(%c)\t", M[i][j], T[i][j]);
if (i == 6 && j == 1)
printf("---");
}
printf(
"\n----------------------------------------------------------------------------------------------");
printf(
"----------------------------------------------------------------------------------------------\n");
}
}
