Add hts_flush() to flush buffered htsFile output data

Implemented by calling through to the various underlying flush routines.
Also add sam_flush() and bcf_flush() wrappers.

NEWS

@@ -1,6 +1,10 @@
 Noteworthy changes in release a.b
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+* New API function hts_flush()/sam_flush()/bcf_flush() for flushing output
+  htsFile/samFile/vcfFile streams. (PR #1326, thanks to John Marshall)
+
+
 Noteworthy changes in release 1.13 (7th July 2021)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

hts.c

@@ -1482,6 +1482,38 @@ int hts_close(htsFile *fp)
     return ret;
 }
 
+int hts_flush(htsFile *fp)
+{
+    if (fp == NULL) return 0;
+
+    switch (fp->format.format) {
+    case binary_format:
+    case bam:
+    case bcf:
+        return bgzf_flush(fp->fp.bgzf);
+
+    case cram:
+        return cram_flush(fp->fp.cram);
+
+    case empty_format:
+    case text_format:
+    case bed:
+    case fasta_format:
+    case fastq_format:
+    case sam:
+    case vcf:
+        if (fp->format.compression != no_compression)
+            return bgzf_flush(fp->fp.bgzf);
+        else
+            return hflush(fp->fp.hfile);
+
+    default:
+        break;
+    }
+
+    return 0;
+}
+
 const htsFormat *hts_get_format(htsFile *fp)
 {
     return fp? &fp->format : NULL;

htslib/hts.h

@@ -599,6 +599,15 @@ htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
 HTSLIB_EXPORT
 htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode);
 
+/*!
+  @abstract  For output streams, flush any buffered data
+  @param fp  The file handle to be flushed
+  @return    0 for success, or negative if an error occurred.
+  @since     1.14
+*/
+HTSLIB_EXPORT
+int hts_flush(htsFile *fp);
+
 /*!
   @abstract  Close a file handle, flushing buffered data for output streams
   @param fp  The file handle to be closed

htslib/sam.h

@@ -1370,6 +1370,7 @@ const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
 
     #define sam_open(fn, mode) (hts_open((fn), (mode)))
     #define sam_open_format(fn, mode, fmt) (hts_open_format((fn), (mode), (fmt)))
+    #define sam_flush(fp) hts_flush((fp))
     #define sam_close(fp) hts_close(fp)
 
     HTSLIB_EXPORT

htslib/vcf.h

@@ -304,6 +304,7 @@ typedef struct bcf1_t {
     typedef htsFile vcfFile;
     #define bcf_open(fn, mode) hts_open((fn), (mode))
     #define vcf_open(fn, mode) hts_open((fn), (mode))
+    #define bcf_flush(fp) hts_flush((fp))
     #define bcf_close(fp) hts_close(fp)
     #define vcf_close(fp) hts_close(fp)