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Try to remove the default depth filter in the pileup. Also fix the version #292

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merged 1 commit into from
Apr 6, 2024
Merged

Try to remove the default depth filter in the pileup. Also fix the version #292

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2 changes: 1 addition & 1 deletion shared/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
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2 changes: 2 additions & 0 deletions src/clair3_pileup.c
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down Expand Up @@ -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;
Expand Down