From 0b7b983e41c2a9761244cd360dea9ced829f9b3d Mon Sep 17 00:00:00 2001
From: Hiruna Samarakoon <hiruna72@gmail.com>
Date: Sun, 13 Sep 2026 12:06:00 +1000
Subject: [PATCH 1/2] add timers around sort and merge output functions and
 print elapsed time

---
 vcfsort.c | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/vcfsort.c b/vcfsort.c
index c333b761..d18e2a92 100644
--- a/vcfsort.c
+++ b/vcfsort.c
@@ -35,6 +35,7 @@
 #include <sys/types.h>
 #include <fcntl.h>
 #include <math.h>
+#include <sys/time.h>
 #ifdef _WIN32
 #include <windows.h>
 #endif
@@ -830,9 +831,22 @@ int main_sort(int argc, char *argv[])
     }
     else args->fname = argv[optind];
 
+    struct timeval t0, t1;
+
     init(args);
+
+    gettimeofday(&t0, NULL);
     sort_blocks(args);
+    gettimeofday(&t1, NULL);
+    fprintf(stderr,"Phase 1 (sort and merge to temporary files): %f seconds\n",
+            ((t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec)) / 1e6);
+
+    gettimeofday(&t0, NULL);
     merge_to_output(args);
+    gettimeofday(&t1, NULL);
+    fprintf(stderr,"Phase 2 (merge temporary files to output): %f seconds\n",
+            ((t1.tv_sec - t0.tv_sec) * 1e6 + (t1.tv_usec - t0.tv_usec)) / 1e6);
+
     destroy(args);
 
     return 0;

From 51305b86a1fa2a92f964d8dcfd6990375fa6729b Mon Sep 17 00:00:00 2001
From: Hiruna Samarakoon <hiruna72@gmail.com>
Date: Sun, 13 Sep 2026 12:27:03 +1000
Subject: [PATCH 2/2] introduce --threads to sort command

---
 doc/bcftools.txt |  3 +++
 vcfsort.c        | 20 ++++++++++++++++++++
 2 files changed, 23 insertions(+)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 32ee1c6a..867107d0 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -3588,6 +3588,9 @@ Transition probabilities:
     Use this directory to store temporary files. If the last six characters of the string DIR are XXXXXX,
     then these are replaced with a string that makes the directory name unique.
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 *-v, --verbosity* 'INT'::
     see *<<common_options,Common Options>>*
 
diff --git a/vcfsort.c b/vcfsort.c
index d18e2a92..a99ccac9 100644
--- a/vcfsort.c
+++ b/vcfsort.c
@@ -44,6 +44,7 @@
 #include <htslib/hts_os.h>
 #include <htslib/hts_defs.h>
 #include <htslib/bgzf.h>
+#include <htslib/thread_pool.h>
 #include "kheap.h"
 #include "bcftools.h"
 
@@ -85,6 +86,8 @@ typedef struct _args_t
     blk_t blk[MAX_TMP_FILES];
     uint32_t tmp_layers[MERGE_LAYERS];
     int write_index;
+    int n_threads;
+    htsThreadPool *tpool;
 }
 args_t;
 
@@ -682,6 +685,15 @@ void merge_to_output(args_t *args)
     htsFile *out = hts_open(output_fname, wmode);
     if (!out) clean_files_and_throw(args, "[%s] Error: cannot open %s\n", __func__, output_fname);
 
+    if ( args->n_threads > 0 )
+    {
+        args->tpool = (htsThreadPool*) calloc(1, sizeof(htsThreadPool));
+        if ( !args->tpool ) clean_files_and_throw(args, "Failed to allocate memory\n");
+        if ( !(args->tpool->pool = hts_tpool_init(args->n_threads)) )
+            clean_files_and_throw(args, "Failed to initialize %d threads\n", args->n_threads);
+        hts_set_opt(out, HTS_OPT_THREAD_POOL, args->tpool);
+    }
+
     fprintf(stderr,"Merging %zd temporary files\n", args->nblk);
     merge_blocks(args, out, output_fname, args->write_index, 0);
     fprintf(stderr,"Done\n");
@@ -708,6 +720,7 @@ static void usage(args_t *args)
 #else
     fprintf(stderr, "    -T, --temp-dir DIR             Temporary files [/tmp/bcftools.XXXXXX]\n");
 #endif
+    fprintf(stderr, "        --threads INT              Use multithreading with INT worker threads [0]\n");
     fprintf(stderr, "    -v, --verbosity INT            Verbosity level\n");
     fprintf(stderr, "    -W, --write-index[=FMT]        Automatically index the output files [off]\n");
     fprintf(stderr, "\n");
@@ -761,6 +774,11 @@ static void destroy(args_t *args)
     bcf_hdr_destroy(args->hdr);
     free(args->mem_block);
     free(args->tmp_dir);
+    if ( args->tpool )
+    {
+        hts_tpool_destroy(args->tpool->pool);
+        free(args->tpool);
+    }
     free(args);
 }
 
@@ -783,6 +801,7 @@ int main_sort(int argc, char *argv[])
         {"help",no_argument,NULL,'h'},
         {"write-index",optional_argument,NULL,'W'},
         {"verbosity",required_argument,NULL,'v'},
+        {"threads",required_argument,NULL,9},
         {0,0,0,0}
     };
     char *tmp;
@@ -790,6 +809,7 @@ int main_sort(int argc, char *argv[])
     {
         switch (c)
         {
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'v':
                 if ( apply_verbosity(optarg) < 0 ) error("Could not parse argument: --verbosity %s\n", optarg);
                 break;