Merge pull request #292 from dpryan79/infinite_maxcnt

Try to remove the default depth filter in the pileup. Also fix the version

shared/utils.py

@@ -248,7 +248,7 @@ def samtools_view_process_from(
         shlex.split("%s view -F 2318 %s %s" % (samtools, bam_file_path, region_str))
     )
 
-def get_header(reference_file_path=None, cmd_fn=None, sample_name="SAMPLE", version='1.0.4', gvcf=False):
+def get_header(reference_file_path=None, cmd_fn=None, sample_name="SAMPLE", version='1.0.7', gvcf=False):
     from textwrap import dedent
 
     if reference_file_path is None or not os.path.exists(reference_file_path):

src/clair3_pileup.c

@@ -7,6 +7,7 @@
 #include <stdio.h>
 #include <stdint.h>
 #include <stdlib.h>
+#include <limits.h>
 #include "htslib/sam.h"
 #include "htslib/faidx.h"
 #include "kvec.h"
@@ -167,6 +168,7 @@ plp_data calculate_clair3_pileup(const char *region, const bam_fset* bam_set, co
     data->min_mapQ = min_mq;
 
     bam_mplp_t mplp = bam_mplp_init(1, read_bam, (void **)& data);
+    bam_mplp_set_maxcnt(mplp, INT_MAX);
 
     const bam_pileup1_t **plp = xalloc(1, sizeof(bam_pileup1_t *), "pileup");
     int ret, pos, tid, n_plp;