[DRAFT] Add bam_aux_remove_if()

Author: jmarshall

htslib/sam.h

@@ -1804,6 +1804,20 @@ BAM record's aux data is corrupt.
 HTSLIB_EXPORT
 uint8_t *bam_aux_remove(bam1_t *b, uint8_t *s);
 
+typedef int bam_aux_filter_func(bam1_t *b, uint8_t *s, void *data);
+
+/// Delete several aux fields from a BAM record
+/** @param b       The BAM record to update
+    @param filter  Pointer to decision function (non-zero means remove)
+    @param data    Pointer to any user data needed by the decision function
+    @return        Number of aux fields removed, or negative on error
+
+Calls @p filter() for each aux field in turn, and removes each aux field
+for which the decision function returns non-zero.
+ */
+HTSLIB_EXPORT
+int bam_aux_remove_if(bam1_t *b, bam_aux_filter_func *filter, void *data);
+
 /// Update or add a string-type tag
 /* @param b    The bam record to update
    @param tag  Tag identifier

sam.c

@@ -4682,6 +4682,39 @@ uint8_t *bam_aux_remove(bam1_t *b, uint8_t *s)
     return NULL;
 }
 
+int bam_aux_remove_if(bam1_t *b, bam_aux_filter_func *remove, void *data)
+{
+    uint8_t *end = b->data + b->l_data;
+    uint8_t *p_from, *p_to;
+    int removed = 0;
+
+    p_from = p_to = bam_get_aux(b);
+
+    while (p_from < end) {
+        uint8_t *next = skip_aux(p_from+2, end);
+        if (next == NULL) goto bad_aux;
+
+        if (remove(b, p_from+2, data)) {
+            removed++;
+        }
+        else {
+            size_t len = next - p_from;
+            if (p_to != p_from) memmove(p_to, p_from, len);
+            p_to += len;
+        }
+
+        p_from = next;
+    }
+
+    b->l_data = p_to - b->data;
+    return removed;
+
+ bad_aux:
+    hts_log_error("Corrupted aux data for read %s", bam_get_qname(b));
+    memset(p_to, '\0', p_from - p_to);
+    return -1;
+}
+
 int bam_aux_update_str(bam1_t *b, const char tag[2], int len, const char *data)
 {
     // FIXME: This is not at all efficient!