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Fix threaded sam_read1 after EOF. #1856

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Fix threaded sam_read1 after EOF. #1856

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15 changes: 14 additions & 1 deletion sam.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3216,6 +3216,7 @@ enum sam_cmd {
SAM_NONE = 0,
SAM_CLOSE,
SAM_CLOSE_DONE,
SAM_AT_EOF,
};

typedef struct SAM_state {
Expand Down Expand Up @@ -3651,6 +3652,7 @@ static void *sam_dispatcher_read(void *vp) {
pthread_mutex_unlock(&fd->command_m);
}

// Submit a NULL sp_bams entry to act as an EOF marker
if (hts_tpool_dispatch(fd->p, fd->q, sam_parse_eof, NULL) < 0)
goto err;

Expand Down Expand Up @@ -4308,14 +4310,25 @@ static inline int sam_read1_sam(htsFile *fp, sam_hdr_t *h, bam1_t *b) {
errno = fd->errcode;
return -2;
}

pthread_mutex_lock(&fd->command_m);
int cmd = fd->command;
pthread_mutex_unlock(&fd->command_m);
if (cmd == SAM_AT_EOF)
return -1;

hts_tpool_result *r = hts_tpool_next_result_wait(fd->q);
if (!r)
return -2;
fd->curr_bam = gb = (sp_bams *)hts_tpool_result_data(r);
hts_tpool_delete_result(r, 0);
}
if (!gb)
if (!gb) {
pthread_mutex_lock(&fd->command_m);
fd->command = SAM_AT_EOF;
pthread_mutex_unlock(&fd->command_m);
return fd->errcode ? -2 : -1;
}
bam1_t *b_array = (bam1_t *)gb->bams;
if (fd->curr_idx < gb->nbams)
if (!bam_copy1(b, &b_array[fd->curr_idx++]))
Expand Down