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Change tabix index type from TBI to CSI, allow chromosome size > 512 Mb #113

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Change tabix index type from TBI to CSI, allow chromosome size > 512 Mb #113

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3ea6b4c
Change tabix index type from TBI to CSI, allow chromosome size > 512 Mb
zoomlion Oct 17, 2025
d645186
Merge pull request #1 from zoomlion/zoomlion-patch-1
zoomlion Oct 17, 2025
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10 changes: 5 additions & 5 deletions coolbox/utilities/bed.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,7 +358,7 @@ def bgz_bed(bed_path, bgz_path):


def index_bed(bgz_path):
cmd = ['tabix', '-p', 'bed', bgz_path]
cmd = ['tabix', '-p', 'bed', bgz_path, '-C']
subp.check_call(cmd)


Expand Down Expand Up @@ -404,8 +404,8 @@ def build_bed_index(file):
bgz_file = file + '.bgz'
log.info(f"Bgzip bed file, save to {bgz_file}")
bgz_bed(file, bgz_file)
if not osp.exists(bgz_file + '.tbi'):
log.info(f"Make tabix of bgz file, save to {bgz_file}.tbi")
if not osp.exists(bgz_file + '.csi'):
log.info(f"Make csi of bgz file, save to {bgz_file}.csi")
index_bed(bgz_file)
return bgz_file

Expand Down Expand Up @@ -504,7 +504,7 @@ def gtf_gz_to_bgz(gz, bgz):
def tabix_index(filename, preset="gff"):
"""Call tabix to create an index for a bgzip-compressed file."""
subp.check_call([
'tabix', '-p', preset, filename
'tabix', '-p', preset, filename, '-C'
])


Expand All @@ -525,7 +525,7 @@ def build_gtf_index(file):
else:
raise IOError(f"GTF track only support GTF file(.gtf or .gtf.gz), got {file}.")

idx_file = bgz_file + ".tbi"
idx_file = bgz_file + ".csi"
if not osp.exists(idx_file):
log.info(f"Tabix index not found, build it in {idx_file}")
tabix_index(bgz_file)
Expand Down