ret->s[1][k+1] = ref[pos + k + 1];
} else ret->s[1][0] = '*';
// write count
- for (j = 0; j < n; ++j) {
- if (score[max1_i*n+j] < 0 && score[max2_i*n+j] < 0) ++ret->cnt_anti;
- else {
- int diff = score[max1_i*n+j] - score[max2_i*n+j];
- if (diff > mi->ambi_thres) ++ret->cnt1;
- else if (diff < -mi->ambi_thres) ++ret->cnt2;
- else ++ret->cnt_ambi;
- }
+ for (i = 0; i < n; ++i) {
+ const bam_pileup1_t *p = pl + i;
+ if (p->indel == ret->indel1) ++ret->cnt1;
+ else if (p->indel == ret->indel2) ++ret->cnt2;
+ else ++ret->cnt_anti;
}
// write gl[]
ret->gl[0] = ret->gl[1] = 0;
printf("%d\t%d\t", max_mapq, n);
printf("%s\t%s\t", r->s[0], r->s[1]);
//printf("%d\t%d\t", r->gl[0], r->gl[1]);
- printf("%d\t%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_ambi, r->cnt_anti);
+ printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);
bam_maqindel_ret_destroy(r);
}
return 0;
between the `reference base' and the `read bases' columns. An indel
occupies an additional line. Each indel line consists of chromosome
name, coordinate, a star, top two high-scoring ins/del sequences, the
-number of reads strongly supporting the first indel, the number of reads
-strongly supporting the second indel, the number of reads that confer
-little information on distinguishing indels and the number of reads that
-contain indels different from the top two ones.
+number of alignments containing the first indel allele, the number of
+alignments containing the second indel allele, and the number of
+alignments containing indels different from the top two alleles.
.B OPTIONS:
.RS
.IP o 2
Reference sequence names and lengths are not acquired from the BAM/SAM header.
.IP o 2
-CIGAR operations N and P may not be properly handled.
+CIGAR operation P is not properly handled at the moment.
.IP o 2
There is a small memory leak in the viewer.
.SH AUTHOR
.PP
-Heng Li from the Sanger Institute is the author of the C version of
-samtools. Bob Handsaker from the Broad Institute implemented the BGZF
-library and Jue Ruan from Beijing Genomics Institute wrote the RAZF
-library. Various people in the 1000Genomes Project contributed to the
-SAM format specification.
+Heng Li from the Sanger Institute wrote the C version of samtools. Bob
+Handsaker from the Broad Institute implemented the BGZF library and Jue
+Ruan from Beijing Genomics Institute wrote the RAZF library. Various
+people in the 1000Genomes Project contributed to the SAM format
+specification.
.SH SEE ALSO
.PP