1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8
markd
  Tue Apr 21 14:09:04 2026 -0700
rework of htslib/UDC integration to use htslib hfile driver mechanism

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 4c517c9854c..507ded3afde 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -80,30 +80,35 @@
  * and call callbackFunc on each bam item retrieved from the file plus callbackData.
  * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. 
  * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
  * the benefit of the callback function, with the open samFile.  
  * refUrl points to the place to grab CRAM reference sequences (if any)
  * cacheDir points to the directory in which CRAM reference sequences are cached */
 
 void bamFetch(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
 	samfile_t **pSamFile);
 /* Open the .bam file, fetch items in the seq:start-end position range,
  * and call callbackFunc on each bam item retrieved from the file plus callbackData.
  * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. 
  * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
  * the benefit of the callback function, with the open samFile.  */
 
+void cramCheckRefs(samfile_t *fh, char *refUrl, char *cacheDir);
+/* Check if all CRAM reference sequences are locally available.  If any are
+ * missing, create pending-download request files and errAbort with a message
+ * telling the user to refresh.  No-op if fh is not CRAM or cacheDir is NULL. */
+
 void bamClose(samfile_t **pSamFile);
 /* Close down a samefile_t */
 
 boolean bamIsRc(const bam1_t *bam);
 /* Return TRUE if alignment is on - strand. */
 
 INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp)
 /* Given an unsigned int containing a number of bases and an offset into an
  * array of BAM-enhanced-CIGAR ASCII characters (operations), store operation 
  * char into *retOp (retOp must not be NULL) and return the number of bases. */
 {
 // decoding lifted from samtools bam.c bam_format1_core(), long may it remain stable:
 #define BAM_DOT_C_OPCODE_STRING "MIDNSHP=X"
 int n = packed>>BAM_CIGAR_SHIFT;
 int opcode = packed & BAM_CIGAR_MASK;