Update devtools/import.py and import/pysam.* for 1.15

Exclude samtools/bam2bcf.[ch] which (starting in samtools 1.15) are only
used by bam_tview.c (which we already exclude) and contain functions that
collide with bcftools. Remove obsolete exclusions for removed items.

In import/pysam.h, add prefixes to several more functions that otherwise
conflict between libcsamtools and libcbcftools. Fixes pysam-developers#1081.

In bcftools/regidx.h, add prefixes to all functions, as these conflict
with those provided by htslib/htslib/regidx.h. This is done locally
within bcftools (rather than via import/pysam.h) as this issue may
be resolved in future bcftools imports by PR samtools/bcftools#865.

Author: jmarshall

bcftools/regidx.h

@@ -65,6 +65,28 @@
 #include <stdio.h>
 #include <inttypes.h>
 
+/* Avoid conflicts with HTSlib's regidx_* functions. */
+#define regidx_destroy bcftools_regidx_destroy
+#define regidx_init bcftools_regidx_init
+#define regidx_init_string bcftools_regidx_init_string
+#define regidx_insert bcftools_regidx_insert
+#define regidx_insert_list bcftools_regidx_insert_list
+#define regidx_nregs bcftools_regidx_nregs
+#define regidx_overlap bcftools_regidx_overlap
+#define regidx_parse_bed bcftools_regidx_parse_bed
+#define regidx_parse_reg bcftools_regidx_parse_reg
+#define regidx_parse_tab bcftools_regidx_parse_tab
+#define regidx_parse_vcf bcftools_regidx_parse_vcf
+#define regidx_push bcftools_regidx_push
+#define regidx_seq_names bcftools_regidx_seq_names
+#define regidx_seq_nregs bcftools_regidx_seq_nregs
+#define regitr_copy bcftools_regitr_copy
+#define regitr_destroy bcftools_regitr_destroy
+#define regitr_init bcftools_regitr_init
+#define regitr_loop bcftools_regitr_loop
+#define regitr_overlap bcftools_regitr_overlap
+#define regitr_reset bcftools_regitr_reset
+
 #ifdef __cplusplus
 extern "C" {
 #endif

devtools/import.py

@@ -18,7 +18,6 @@
 EXCLUDE = {
     "samtools": (
         "test", "misc",
-        "razip.c",
         "bgzip.c",
         "main.c",
         "calDepth.c",
@@ -27,8 +26,8 @@
         "bam_tview.h",
         "bam_tview_html.c",
         "bam_tview_curses.c",
-        "bamcheck.c",
-        "chk_indel.c",
+        "bam2bcf.c",
+        "bam2bcf.h",
         "vcf-miniview.c",
     ),
     "bcftools": (

import/pysam.h

@@ -65,7 +65,11 @@ extern int @pysam@_main(int argc, char *argv[]);
     to collisions and wrong functions being called. #define these names so the
     actual symbol names include distinct prefixes to avoid collisions.
  */
+#define main_consensus @pysam@_main_consensus
 #define main_reheader @pysam@_main_reheader
+#define bam_smpl_init @pysam@_bam_smpl_init
+#define bam_smpl_destroy @pysam@_bam_smpl_destroy
+#define read_file_list @pysam@_read_file_list
 
 #endif