not all region return when using a bed file

[FunGeST]

Hi,

I am using the perbase base-depth using a bed file as site list and --keep-zeros to get info for all my regions described in the bed file, however, the output file only contain part of those region

bed file includes 134487 regions while the output file only reference

bed file extract chr1 930285 930285 chr1_930285_930285_G_A chr1 935896 935896 chr1_935896_935896_G_A chr1 939436 939436 chr1_939436_939436_C_CT chr1 942143 942143 chr1_942143_942143_C_G chr1 942231 942231 chr1_942231_942231_C_T chr1 942469 942469 chr1_942469_942469_C_T chr1 942485 942485 chr1_942485_942485_C_T chr1 942652 942652 chr1_942652_942652_C_G

output file extract REF POS DEPTH A C G T N INS DEL REF_SKIP FAIL NEAR_MAX_DEPTH chr1 944135 147 0 0 0 147 0 0 0 0 0 false chr1 959009 223 0 0 0 223 0 0 0 0 0 false chr1 959010 226 0 0 0 226 0 0 0 0 0 false chr1 959011 226 0 226 0 0 0 0 0 0 0 false chr1 959012 224 0 0 224 0 0 0 0 0 0 false chr1 959013 218 0 0 218 0 0 0 0 0 0 false chr1 959014 216 216 0 0 0 0 0 0 0 0 false chr1 959015 217 0 217 0 0 0 0 0 0 0 false chr1 959016 216 0 0 0 216 0 0 0 0 0 false chr1 959017 215 0 215 0 0 0 0 0 0 0 false chr1 959018 217 0 0 217 0 0 0 0 0 1 false chr1 959019 215 0 0 215 0 0 0 0 0 1 false

Any idea why we miss the corresponding region? Here is my command line => perbase base-depth --mate-fix --ref-fasta hg38.fa -F 3848 --keep-zeros -b vcf_HCA_region.bed -Q 10 -q 40 -t 32 DRAGEN_LINKTOBAM/EN00003608_CHC06597T.bam -Z -o EN00003608_CHC06597T_output.tsv.gz

[sstadick]

@FunGeST - see version 0.10.0 with the fix from @biermanr