Remove the mpileup BAM_CREF_SKIP filter.

Mpileup removes alignments using the cigar ref skip operator ("N").
This was originally added in 2011 in samtools/samtools#d1643d6 with
the commit message of "fixed a bug in indel calling related to
unmapped and refskip reads".

Unfortunately I don't know what that bug was, but removing the code
shows it still works (at least for some data!).  We need better
understanding of what's going on and why it was added, so perhaps we
should add a command line option to control this instead?

Fixes samtools#2277

Author: jkbonfield

Diff for: bam2bcf_edlib.c

@@ -1559,19 +1559,10 @@ int bcf_edlib_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
                     }
                 }
 
-                int qbeg, qpos, qend, tbeg, tend, kk;
+                int qbeg, qpos, qend, tbeg, tend;
                 uint8_t *seq = bam_get_seq(p->b);
-                uint32_t *cigar = bam_get_cigar(p->b);
                 if (p->b->core.flag & BAM_FUNMAP) continue;
 
-                // FIXME: the following loop should be better moved outside;
-                // nonetheless, realignment should be much slower anyway.
-                for (kk = 0; kk < p->b->core.n_cigar; ++kk)
-                    if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP)
-                        break;
-                if (kk < p->b->core.n_cigar)
-                    continue;
-
                 // determine the start and end of sequences for alignment
                 int left2 = left, right2 = right;
                 int min_win_size = MAX(-biggest_del, biggest_ins);

Diff for: bam2bcf_indel.c

@@ -845,19 +845,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos,
                     }
                 }
 
-                int qbeg, qpos, qend, tbeg, tend, kk;
+                int qbeg, qpos, qend, tbeg, tend;
                 uint8_t *seq = bam_get_seq(p->b);
-                uint32_t *cigar = bam_get_cigar(p->b);
                 if (p->b->core.flag & BAM_FUNMAP) continue;
 
-                // FIXME: the following loop should be better moved outside;
-                // nonetheless, realignment should be much slower anyway.
-                for (kk = 0; kk < p->b->core.n_cigar; ++kk)
-                    if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP)
-                        break;
-                if (kk < p->b->core.n_cigar)
-                    continue;
-
                 // determine the start and end of sequences for alignment
                 // FIXME: loops over CIGAR multiple times
                 int left2 = left, right2 = right;