Repeated sample name (SM-tag) issue with BASICFILTERING_MUTECT

[soccin]

Description of the bug

BASICFILTERING_MUTECT seems to also have problems with BAMs that have multiple @RG lines in them. It is not properly de-duping the SM tags. In the .command.sh file you can see the issue:

#!/bin/bash -euo pipefail
filter_mutect.py \
        --totaldepth 5 --alleledepth 3 --tnRatio 5 --variantfraction 0.01 \
        --inputVcf C_CN5Y66_T003_d03___C_CN5Y66_N901_dZ_IM7.mutect.vcf \
        --inputTxt C_CN5Y66_T003_d03___C_CN5Y66_N901_dZ_IM7.mutect.txt \
        --tsampleName s_C_CN5Y66_T003_d03
s_C_CN5Y66_T003_d03 \
        --hotspotVcf hotspot-list-union-v1-v2.vcf \
        --refFasta b37.fasta

The sample name s_C_CN5Y66_T003_d03 is repeated twice.

Command used and terminal output

I am attaching a sample input.csv file with a problem bam.

Relevant files

bug002.csv

System information

odin branch: stage, commit: 3adbfa4.