From 7c013e6aec4e9b41cf48a5864a5bdec7a9309fc4 Mon Sep 17 00:00:00 2001
From: Aidan Bickford <aidan.bickford@gmail.com>
Date: Tue, 11 Jan 2022 14:46:21 -0700
Subject: [PATCH 1/4] Add progress callbacks to index creation

---
 cram/cram_index.c | 10 +++++++++-
 cram/cram_index.h |  4 +++-
 htslib/hts.h      |  3 +++
 htslib/sam.h      | 14 ++++++++++++++
 htslib/tbx.h      |  7 ++++++-
 sam.c             | 24 ++++++++++++++++++------
 tbx.c             | 26 ++++++++++++++++++++++----
 vcf.c             |  2 +-
 8 files changed, 76 insertions(+), 14 deletions(-)

diff --git a/cram/cram_index.c b/cram/cram_index.c
index 45d420df2..470eb5ac7 100644
--- a/cram/cram_index.c
+++ b/cram/cram_index.c
@@ -738,9 +738,10 @@ int cram_index_container(cram_fd *fd,
  * Returns 0 on success,
  *         negative on failure (-1 for read failure, -4 for write failure)
  */
-int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
+int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx, const file_progress_func progress_fn, void *progress_data) {
     cram_container *c;
     off_t cpos, hpos;
+    off_t ppos = 0;
     BGZF *fp;
     kstring_t fn_idx_str = {0};
     int64_t last_ref = -9, last_start = -9;
@@ -771,6 +772,13 @@ int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
 
         hpos = htell(fd->fp);
 
+        if (progress_fn && hpos != ppos) {
+            if (progress_fn(hpos, progress_data) != 0) {
+                return -5;
+            }
+            ppos = hpos;
+        }
+
         if (!(c->comp_hdr_block = cram_read_block(fd)))
             return -1;
         assert(c->comp_hdr_block->content_type == COMPRESSION_HEADER);
diff --git a/cram/cram_index.h b/cram/cram_index.h
index 5fa1154f5..9eb9d01b5 100644
--- a/cram/cram_index.h
+++ b/cram/cram_index.h
@@ -87,12 +87,14 @@ int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
  * fd is a newly opened cram file that we wish to index.
  * fn_base is the filename of the associated CRAM file.
  * fn_idx is the filename of the index file to be written;
+ * progress_fn is an optional callback which will be called periodically with the current working offset into the file 
+ * progress_data is the optional data passed to the progress_fn 
  * if NULL, we add ".crai" to fn_base to get the index filename.
  *
  * Returns 0 on success,
  *         negative on failure (-1 for read failure, -4 for write failure)
  */
-int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx);
+int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx, const file_progress_func progress_fn, void *progress_data);
 
 /*
  * Adds a single slice to the index.
diff --git a/htslib/hts.h b/htslib/hts.h
index 48c263cab..193fa7111 100644
--- a/htslib/hts.h
+++ b/htslib/hts.h
@@ -59,6 +59,9 @@ struct hFILE;
 struct hts_tpool;
 struct sam_hdr_t;
 
+
+typedef int (*file_progress_func)(int64_t current_pos, void *data);
+
 /**
  * @hideinitializer
  * Deprecated macro to expand a dynamic array of a given type
diff --git a/htslib/sam.h b/htslib/sam.h
index 79ac26e4b..7d12dc145 100644
--- a/htslib/sam.h
+++ b/htslib/sam.h
@@ -1237,6 +1237,20 @@ int sam_index_build2(const char *fn, const char *fnidx, int min_shift) HTS_RESUL
 HTSLIB_EXPORT
 int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads) HTS_RESULT_USED;
 
+/// Generate and save an index to a specific file
+/** @param fn        Input BAM/CRAM/etc filename
+    @param fnidx     Output filename, or NULL to add .bai/.csi/etc to @a fn
+    @param min_shift Positive to generate CSI, or 0 to generate BAI
+    @param nthreads  Number of threads to use when building the index
+    @param progress_fn  Funciton to call with progress updates
+    @param progress_data  Data to pass to the progress function
+    @return  0 if successful, or negative if an error occurred (see
+             sam_index_build for error codes)
+*/
+HTSLIB_EXPORT
+int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthreads, const file_progress_func progress_fn, void* progress_data) HTS_RESULT_USED;
+
+
 /// Free a SAM iterator
 /// @param iter     Iterator to free
 #define sam_itr_destroy(iter) hts_itr_destroy(iter)
diff --git a/htslib/tbx.h b/htslib/tbx.h
index 9b9e111b9..173a9e6e1 100644
--- a/htslib/tbx.h
+++ b/htslib/tbx.h
@@ -52,6 +52,7 @@ typedef struct tbx_t {
     void *dict;
 } tbx_t;
 
+
 extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf;
 
     #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
@@ -75,7 +76,7 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
     via tbx_destroy() when it is no longer needed.
 */
     HTSLIB_EXPORT
-    tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf);
+    tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf, const file_progress_func progress_fn, void *progress_data);
 /*
  * All tbx_index_build* methods return: 0 (success), -1 (general failure) or -2 (compression not BGZF)
  */
@@ -88,6 +89,10 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
     HTSLIB_EXPORT
     int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf);
 
+    HTSLIB_EXPORT
+    int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf, 
+        const file_progress_func progress_fn, void *progress_data);
+
 
 /// Load or stream a .tbi or .csi index
 /** @param fn     Name of the data file corresponding to the index
diff --git a/sam.c b/sam.c
index 393a3b22e..b9b618607 100644
--- a/sam.c
+++ b/sam.c
@@ -923,9 +923,10 @@ int bam_set_qname(bam1_t *rec, const char *qname)
  *** BAM indexing ***
  ********************/
 
-static hts_idx_t *sam_index(htsFile *fp, int min_shift)
+static hts_idx_t *sam_index(htsFile *fp, int min_shift, const file_progress_func progress_fn, void* progress_data)
 {
     int n_lvls, i, fmt, ret;
+    int64_t last_block_address = 0;
     bam1_t *b;
     hts_idx_t *idx;
     sam_hdr_t *h;
@@ -944,6 +945,12 @@ static hts_idx_t *sam_index(htsFile *fp, int min_shift)
     idx = hts_idx_init(h->n_targets, fmt, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls);
     b = bam_init1();
     while ((ret = sam_read1(fp, h, b)) >= 0) {
+        if (progress_fn && fp->fp.bgzf->block_address != last_block_address) {
+            if (progress_fn(fp->fp.bgzf->block_address, progress_data) != 0) {
+                goto err;
+            }
+            last_block_address = fp->fp.bgzf->block_address;
+        }
         ret = hts_idx_push(idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp->fp.bgzf), !(b->core.flag&BAM_FUNMAP));
         if (ret < 0) { // unsorted or doesn't fit
             hts_log_error("Read '%s' with ref_name='%s', ref_length=%"PRIhts_pos", flags=%d, pos=%"PRIhts_pos" cannot be indexed", bam_get_qname(b), sam_hdr_tid2name(h, b->core.tid), sam_hdr_tid2len(h, b->core.tid), b->core.flag, b->core.pos+1);
@@ -963,7 +970,7 @@ static hts_idx_t *sam_index(htsFile *fp, int min_shift)
     return NULL;
 }
 
-int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads)
+int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthreads, const file_progress_func progress_fn, void* progress_data)
 {
     hts_idx_t *idx;
     htsFile *fp;
@@ -976,7 +983,7 @@ int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthre
     switch (fp->format.format) {
     case cram:
 
-        ret = cram_index_build(fp->fp.cram, fn, fnidx);
+        ret = cram_index_build(fp->fp.cram, fn, fnidx, progress_fn, progress_data);
         break;
 
     case bam:
@@ -987,7 +994,7 @@ int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthre
             ret = -1;
             break;
         }
-        idx = sam_index(fp, min_shift);
+        idx = sam_index(fp, min_shift, progress_fn, progress_data);
         if (idx) {
             ret = hts_idx_save_as(idx, fn, fnidx, (min_shift > 0)? HTS_FMT_CSI : HTS_FMT_BAI);
             if (ret < 0) ret = -4;
@@ -1005,9 +1012,14 @@ int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthre
     return ret;
 }
 
-int sam_index_build2(const char *fn, const char *fnidx, int min_shift)
+int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads)
 {
-    return sam_index_build3(fn, fnidx, min_shift, 0);
+    return sam_index_build3(fn, fnidx, min_shift, nthreads);
+}
+
+int sam_index_build2(const char *fn, int min_shift)
+{
+    return sam_index_build3(fn, NULL, min_shift, 0);
 }
 
 int sam_index_build(const char *fn, int min_shift)
diff --git a/tbx.c b/tbx.c
index 0d486ad9c..10d838158 100644
--- a/tbx.c
+++ b/tbx.c
@@ -285,7 +285,8 @@ static int adjust_n_lvls(int min_shift, int n_lvls, int64_t max_len)
     return n_lvls;
 }
 
-tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf)
+tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf,
+                 const file_progress_func progress_fn, void *progress_data)
 {
     tbx_t *tbx;
     kstring_t str;
@@ -294,6 +295,7 @@ tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf)
     uint64_t last_off = 0;
     tbx_intv_t intv;
     int64_t max_ref_len = 0;
+    int64_t last_block_address = 0;
 
     str.s = 0; str.l = str.m = 0;
     tbx = (tbx_t*)calloc(1, sizeof(tbx_t));
@@ -303,6 +305,14 @@ tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf)
     else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_TBI;
     while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) {
         ++lineno;
+
+        if (last_block_address != fp->block_address) {
+            if (progress_fn && progress_fn(fp->block_address, progress_data) != 0) {
+                goto fail;
+            }
+            last_block_address = fp->block_address;
+        }
+
         if (str.s[0] == tbx->conf.meta_char && fmt == HTS_FMT_CSI) {
             switch (tbx->conf.preset) {
                 case TBX_SAM:
@@ -363,6 +373,13 @@ void tbx_destroy(tbx_t *tbx)
 }
 
 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf)
+{
+    tbx_index_build4(fn, fnidx, min_shift, n_threads, conf, NULL, NULL);
+}
+
+int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads,
+                     const tbx_conf_t *conf, const file_progress_func progress_fn,
+                     void *progress_data)
 {
     tbx_t *tbx;
     BGZF *fp;
@@ -370,7 +387,7 @@ int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_thr
     if ((fp = bgzf_open(fn, "r")) == 0) return -1;
     if ( n_threads ) bgzf_mt(fp, n_threads, 256);
     if ( bgzf_compression(fp) != bgzf ) { bgzf_close(fp); return -2; }
-    tbx = tbx_index(fp, min_shift, conf);
+    tbx = tbx_index(fp, min_shift, conf, progress_fn, progress_data);
     bgzf_close(fp);
     if ( !tbx ) return -1;
     ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI);
@@ -378,14 +395,15 @@ int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_thr
     return ret;
 }
 
+
 int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf)
 {
-    return tbx_index_build3(fn, fnidx, min_shift, 0, conf);
+    return tbx_index_build4(fn, fnidx, min_shift, 0, conf, NULL, NULL);
 }
 
 int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf)
 {
-    return tbx_index_build3(fn, NULL, min_shift, 0, conf);
+    return tbx_index_build4(fn, NULL, min_shift, 0, conf, NULL, NULL);
 }
 
 static tbx_t *index_load(const char *fn, const char *fnidx, int flags)
diff --git a/vcf.c b/vcf.c
index 0d59be6e6..cc0c558f5 100644
--- a/vcf.c
+++ b/vcf.c
@@ -3403,7 +3403,7 @@ int bcf_index_build3(const char *fn, const char *fnidx, int min_shift, int n_thr
             break;
 
         case vcf:
-            tbx = tbx_index(hts_get_bgzfp(fp), min_shift, &tbx_conf_vcf);
+            tbx = tbx_index(hts_get_bgzfp(fp), min_shift, &tbx_conf_vcf, NULL, NULL);
             if (tbx) {
                 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0 ? HTS_FMT_CSI : HTS_FMT_TBI);
                 if (ret < 0) ret = -4;

From efc2c974fcc8c2c2341dbee423715abb2f46d822 Mon Sep 17 00:00:00 2001
From: Aidan Bickford <aidan.bickford@gmail.com>
Date: Tue, 11 Jan 2022 17:19:21 -0700
Subject: [PATCH 2/4] Update indexing function names

---
 sam.c | 8 ++++----
 tbx.c | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/sam.c b/sam.c
index b9b618607..a75e233ee 100644
--- a/sam.c
+++ b/sam.c
@@ -1014,17 +1014,17 @@ int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthre
 
 int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthreads)
 {
-    return sam_index_build3(fn, fnidx, min_shift, nthreads);
+    return sam_index_build4(fn, fnidx, min_shift, nthreads, NULL, NULL);
 }
 
-int sam_index_build2(const char *fn, int min_shift)
+int sam_index_build2(const char *fn, const char *fnidx, int min_shift)
 {
-    return sam_index_build3(fn, NULL, min_shift, 0);
+    return sam_index_build4(fn, fnidx, min_shift, 0, NULL, NULL);
 }
 
 int sam_index_build(const char *fn, int min_shift)
 {
-    return sam_index_build3(fn, NULL, min_shift, 0);
+    return sam_index_build4(fn, NULL, min_shift, 0, NULL, NULL);
 }
 
 // Provide bam_index_build() symbol for binary compatibility with earlier HTSlib
diff --git a/tbx.c b/tbx.c
index 10d838158..90e351504 100644
--- a/tbx.c
+++ b/tbx.c
@@ -374,7 +374,7 @@ void tbx_destroy(tbx_t *tbx)
 
 int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf)
 {
-    tbx_index_build4(fn, fnidx, min_shift, n_threads, conf, NULL, NULL);
+    return tbx_index_build4(fn, fnidx, min_shift, n_threads, conf, NULL, NULL);
 }
 
 int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads,

From 4222d2895cdcb8e80a01cd3dac86437e7ee068dd Mon Sep 17 00:00:00 2001
From: Aidan Bickford <aidan.bickford@gmail.com>
Date: Wed, 12 Jan 2022 08:33:35 -0700
Subject: [PATCH 3/4] Remove trailing spaces

---
 cram/cram_index.h | 4 ++--
 htslib/tbx.h      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/cram/cram_index.h b/cram/cram_index.h
index 9eb9d01b5..fe2e951b2 100644
--- a/cram/cram_index.h
+++ b/cram/cram_index.h
@@ -87,8 +87,8 @@ int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
  * fd is a newly opened cram file that we wish to index.
  * fn_base is the filename of the associated CRAM file.
  * fn_idx is the filename of the index file to be written;
- * progress_fn is an optional callback which will be called periodically with the current working offset into the file 
- * progress_data is the optional data passed to the progress_fn 
+ * progress_fn is an optional callback which will be called periodically with the current working offset into the file
+ * progress_data is the optional data passed to the progress_fn
  * if NULL, we add ".crai" to fn_base to get the index filename.
  *
  * Returns 0 on success,
diff --git a/htslib/tbx.h b/htslib/tbx.h
index 173a9e6e1..fd5be4d2d 100644
--- a/htslib/tbx.h
+++ b/htslib/tbx.h
@@ -90,7 +90,7 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
     int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf);
 
     HTSLIB_EXPORT
-    int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf, 
+    int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf,
         const file_progress_func progress_fn, void *progress_data);
 
 

From 19cbba400736a36a7f00f4e7f70477cc3de9b5f1 Mon Sep 17 00:00:00 2001
From: Aidan Bickford <aidan.bickford@gmail.com>
Date: Wed, 26 Jan 2022 14:46:33 -0700
Subject: [PATCH 4/4] Update progress call back typedef name, add new function
 for tbx_index2 to preserve API and ABI

---
 cram/cram_index.c |  2 +-
 cram/cram_index.h |  2 +-
 htslib/hts.h      |  2 +-
 htslib/sam.h      |  2 +-
 htslib/tbx.h      |  8 ++++++--
 sam.c             |  4 ++--
 tbx.c             | 13 +++++++++----
 vcf.c             |  2 +-
 8 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/cram/cram_index.c b/cram/cram_index.c
index 470eb5ac7..c8a5054d1 100644
--- a/cram/cram_index.c
+++ b/cram/cram_index.c
@@ -738,7 +738,7 @@ int cram_index_container(cram_fd *fd,
  * Returns 0 on success,
  *         negative on failure (-1 for read failure, -4 for write failure)
  */
-int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx, const file_progress_func progress_fn, void *progress_data) {
+int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx, const hts_progress_callback progress_fn, void *progress_data) {
     cram_container *c;
     off_t cpos, hpos;
     off_t ppos = 0;
diff --git a/cram/cram_index.h b/cram/cram_index.h
index fe2e951b2..d54cf78c0 100644
--- a/cram/cram_index.h
+++ b/cram/cram_index.h
@@ -94,7 +94,7 @@ int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
  * Returns 0 on success,
  *         negative on failure (-1 for read failure, -4 for write failure)
  */
-int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx, const file_progress_func progress_fn, void *progress_data);
+int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx, const hts_progress_callback progress_fn, void *progress_data);
 
 /*
  * Adds a single slice to the index.
diff --git a/htslib/hts.h b/htslib/hts.h
index 193fa7111..9f74cb614 100644
--- a/htslib/hts.h
+++ b/htslib/hts.h
@@ -60,7 +60,7 @@ struct hts_tpool;
 struct sam_hdr_t;
 
 
-typedef int (*file_progress_func)(int64_t current_pos, void *data);
+typedef int (*hts_progress_callback)(int64_t current_pos, void *data);
 
 /**
  * @hideinitializer
diff --git a/htslib/sam.h b/htslib/sam.h
index 7d12dc145..397e9e021 100644
--- a/htslib/sam.h
+++ b/htslib/sam.h
@@ -1248,7 +1248,7 @@ int sam_index_build3(const char *fn, const char *fnidx, int min_shift, int nthre
              sam_index_build for error codes)
 */
 HTSLIB_EXPORT
-int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthreads, const file_progress_func progress_fn, void* progress_data) HTS_RESULT_USED;
+int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthreads, const hts_progress_callback progress_fn, void* progress_data) HTS_RESULT_USED;
 
 
 /// Free a SAM iterator
diff --git a/htslib/tbx.h b/htslib/tbx.h
index fd5be4d2d..0502481b1 100644
--- a/htslib/tbx.h
+++ b/htslib/tbx.h
@@ -76,7 +76,11 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
     via tbx_destroy() when it is no longer needed.
 */
     HTSLIB_EXPORT
-    tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf, const file_progress_func progress_fn, void *progress_data);
+    tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf);
+
+    HTSLIB_EXPORT
+    tbx_t *tbx_index2(BGZF *fp, int min_shift, const tbx_conf_t *conf, const hts_progress_callback progress_fn, void *progress_data);
+
 /*
  * All tbx_index_build* methods return: 0 (success), -1 (general failure) or -2 (compression not BGZF)
  */
@@ -91,7 +95,7 @@ extern const tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sa
 
     HTSLIB_EXPORT
     int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads, const tbx_conf_t *conf,
-        const file_progress_func progress_fn, void *progress_data);
+        const hts_progress_callback progress_fn, void *progress_data);
 
 
 /// Load or stream a .tbi or .csi index
diff --git a/sam.c b/sam.c
index a75e233ee..cd03e421f 100644
--- a/sam.c
+++ b/sam.c
@@ -923,7 +923,7 @@ int bam_set_qname(bam1_t *rec, const char *qname)
  *** BAM indexing ***
  ********************/
 
-static hts_idx_t *sam_index(htsFile *fp, int min_shift, const file_progress_func progress_fn, void* progress_data)
+static hts_idx_t *sam_index(htsFile *fp, int min_shift, const hts_progress_callback progress_fn, void* progress_data)
 {
     int n_lvls, i, fmt, ret;
     int64_t last_block_address = 0;
@@ -970,7 +970,7 @@ static hts_idx_t *sam_index(htsFile *fp, int min_shift, const file_progress_func
     return NULL;
 }
 
-int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthreads, const file_progress_func progress_fn, void* progress_data)
+int sam_index_build4(const char *fn, const char *fnidx, int min_shift, int nthreads, const hts_progress_callback progress_fn, void* progress_data)
 {
     hts_idx_t *idx;
     htsFile *fp;
diff --git a/tbx.c b/tbx.c
index 90e351504..d97ff59cd 100644
--- a/tbx.c
+++ b/tbx.c
@@ -285,8 +285,13 @@ static int adjust_n_lvls(int min_shift, int n_lvls, int64_t max_len)
     return n_lvls;
 }
 
-tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf,
-                 const file_progress_func progress_fn, void *progress_data)
+tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf)
+{
+    return tbx_index2(fp, min_shift, conf, NULL, NULL);
+}
+
+tbx_t *tbx_index2(BGZF *fp, int min_shift, const tbx_conf_t *conf,
+                 const hts_progress_callback progress_fn, void *progress_data)
 {
     tbx_t *tbx;
     kstring_t str;
@@ -378,7 +383,7 @@ int tbx_index_build3(const char *fn, const char *fnidx, int min_shift, int n_thr
 }
 
 int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_threads,
-                     const tbx_conf_t *conf, const file_progress_func progress_fn,
+                     const tbx_conf_t *conf, const hts_progress_callback progress_fn,
                      void *progress_data)
 {
     tbx_t *tbx;
@@ -387,7 +392,7 @@ int tbx_index_build4(const char *fn, const char *fnidx, int min_shift, int n_thr
     if ((fp = bgzf_open(fn, "r")) == 0) return -1;
     if ( n_threads ) bgzf_mt(fp, n_threads, 256);
     if ( bgzf_compression(fp) != bgzf ) { bgzf_close(fp); return -2; }
-    tbx = tbx_index(fp, min_shift, conf, progress_fn, progress_data);
+    tbx = tbx_index2(fp, min_shift, conf, progress_fn, progress_data);
     bgzf_close(fp);
     if ( !tbx ) return -1;
     ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI);
diff --git a/vcf.c b/vcf.c
index cc0c558f5..0d59be6e6 100644
--- a/vcf.c
+++ b/vcf.c
@@ -3403,7 +3403,7 @@ int bcf_index_build3(const char *fn, const char *fnidx, int min_shift, int n_thr
             break;
 
         case vcf:
-            tbx = tbx_index(hts_get_bgzfp(fp), min_shift, &tbx_conf_vcf, NULL, NULL);
+            tbx = tbx_index(hts_get_bgzfp(fp), min_shift, &tbx_conf_vcf);
             if (tbx) {
                 ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0 ? HTS_FMT_CSI : HTS_FMT_TBI);
                 if (ret < 0) ret = -4;