Ensure NUL termination of Z/H data in sam_format_aux1; fix base mod s…

…tate reuse

Ensure NUL termination of Z/H data in sam_format_aux1

Avoid failure to get base modifications when reusing the
hts_base_mod_state struct.

Minor comment updates

htslib/sam.h

@@ -1,7 +1,7 @@
 /// @file htslib/sam.h
 /// High-level SAM/BAM/CRAM sequence file operations.
 /*
-    Copyright (C) 2008, 2009, 2013-2022 Genome Research Ltd.
+    Copyright (C) 2008, 2009, 2013-2023 Genome Research Ltd.
     Copyright (C) 2010, 2012, 2013 Broad Institute.
 
     Author: Heng Li <[email protected]>
@@ -1414,7 +1414,7 @@ const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
 /** @param fp    Pointer to the destination file
  *  @param h     Pointer to the header structure previously read
  *  @param b     Pointer to the record to be written
- *  @return >= 0 on successfully writing the record, -1 on error
+ *  @return >= 0 on successfully writing the record, -ve on error
  */
     HTSLIB_EXPORT
     int sam_write1(samFile *fp, const sam_hdr_t *h, const bam1_t *b) HTS_RESULT_USED;
@@ -1519,6 +1519,7 @@ static inline const uint8_t *sam_format_aux1(const uint8_t *key,
         r |= kputc_(type, ks) < 0;
         r |= kputc_(':', ks) < 0;
         while (s < end && *s) r |= kputc_(*s++, ks) < 0;
+        r |= kputsn("", 0, ks) < 0;     //ensures NUL termination
         if (s >= end)
             goto bad_aux;
         ++s;
@@ -2286,6 +2287,7 @@ int bam_mods_at_next_pos(const bam1_t *b, hts_base_mod_state *state,
  * @param state    The base modification state pointer.
  * @param mods     A supplied array for returning base modifications
  * @param n_mods   The size of the mods array
+ * @param pos      Pointer holding position of modification in sequence
  * @return The number of modifications found on success,
  *         0 if no more modifications are present,
  *         -1 on failure.

sam.c

@@ -6215,6 +6215,10 @@ static int seqi_rc[] = { 0,8,4,12,2,10,6,14,1,9,5,13,3,11,7,15 };
  *
  */
 int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state) {
+
+    //reset position, else upcoming calls may fail on seq pos - length comparison
+    state->seq_pos = 0;
+
     // Read MM and ML tags
     uint8_t *mm = bam_aux_get(b, "MM");
     if (!mm) mm = bam_aux_get(b, "Mm");
@@ -6244,8 +6248,6 @@ int bam_parse_basemod(const bam1_t *b, hts_base_mod_state *state) {
     uint8_t *ml_end = ml ? ml+6 + le_to_u32(ml+2) : NULL;
     if (ml) ml += 6;
 
-    state->seq_pos = 0;
-
     // Aggregate freqs of ACGTN if reversed, to get final-delta (later)
     int freq[16];
     if (b->core.flag & BAM_FREVERSE)