conda sambamba 1.0 is running slower than conda sambamba 0.6

[ericpanyc]

The bug is described as the title.

sambamba 0.6.6 from conda

`time ~/miniconda3/envs/sambamba-0.6/bin/sambamba depth region -F 'not unmapped and not secondary_alignment and not duplicate and not failed_quality_control and mapping_quality > 9' -t 4 -c 0 -T 10 -L /mnt/efs/Annotations/References/Hsapiens/GRCh38/bed/refseq_allexons_extend5_ucsc_hg38.bed -o ./test_sambamba_depth_region_one_thresh.bed ./PLM00993810-B-D_20230306_TES_Clinical1.0-dragen.hg38.bam
Processing reference #1 (chr1)
Processing reference #2 (chr2)
Processing reference #3 (chr3)
Processing reference #4 (chr4)
Processing reference #5 (chr5)
Processing reference #6 (chr6)
Processing reference #7 (chr7)
Processing reference #8 (chr8)
Processing reference #9 (chr9)
Processing reference #10 (chr10)
Processing reference #11 (chr11)
Processing reference #12 (chr12)
Processing reference #13 (chr13)
Processing reference #14 (chr14)
Processing reference #15 (chr15)
Processing reference #16 (chr16)
Processing reference #17 (chr17)
Processing reference #18 (chr18)
Processing reference #19 (chr19)
Processing reference #20 (chr20)
Processing reference #21 (chr21)
Processing reference #22 (chr22)
Processing reference #23 (chrX)
Processing reference #24 (chrY)

real 6m35.792s
user 13m50.081s
sys 0m14.050s`

sambamba 1.0.0 from conda

`time ~/miniconda3/envs/sambamba-1.0/bin/sambamba depth region -F 'not unmapped and not secondary_alignment and not duplicate and not failed_quality_control and mapping_quality > 9' -t 4 -c 0 -T 10 -L /mnt/efs/Annotations/References/Hsapiens/GRCh38/bed/refseq_allexons_extend5_ucsc_hg38.bed -o ./test_sambamba1.0_depth_region_one_thresh.bed ./PLM00993810-B-D_20230306_TES_Clinical1.0-dragen.hg38.bam

sambamba 1.0.0
by Artem Tarasov and Pjotr Prins (C) 2012-2022
LDC 1.28.1 / DMD v2.098.1 / LLVM12.0.0 / bootstrap LDC - the LLVM D compiler (1.28.1)

Processing reference #1 (chr1)
Processing reference #2 (chr2)
Processing reference #3 (chr3)
Processing reference #4 (chr4)
Processing reference #5 (chr5)
Processing reference #6 (chr6)
Processing reference #7 (chr7)
Processing reference #8 (chr8)
Processing reference #9 (chr9)
Processing reference #10 (chr10)
Processing reference #11 (chr11)
Processing reference #12 (chr12)
Processing reference #13 (chr13)
Processing reference #14 (chr14)
Processing reference #15 (chr15)
Processing reference #16 (chr16)
Processing reference #17 (chr17)
Processing reference #18 (chr18)
Processing reference #19 (chr19)
Processing reference #20 (chr20)
Processing reference #21 (chr21)
Processing reference #22 (chr22)
Processing reference #23 (chrX)
Processing reference #24 (chrY)

real 40m32.600s
user 46m37.605s
sys 0m16.209s`

I can reproduce the issue on other x86_64 instances.

[pjotrp]

Please contact conda. Or try the actual releases you can download from https://github.com/biod/sambamba/releases