diff --git a/shared/utils.py b/shared/utils.py index c5c2d42..e9db06a 100644 --- a/shared/utils.py +++ b/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): diff --git a/src/clair3_pileup.c b/src/clair3_pileup.c index 5969336..b5c77a1 100644 --- a/src/clair3_pileup.c +++ b/src/clair3_pileup.c @@ -7,6 +7,7 @@ #include #include #include +#include #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;