list index out of range

[agos316]

Hi,
Everything seems to work until selection of candidates for full alignment.

"var_qual_cut_off = variant_qual_list[:int(var_pct_full * len(variant_qual_list))][-1]
IndexError: list index out of range"

Is there a way to bypass this or the reason for this error?

thanks

Marc

[zhengzhenxian]

Hi, Marc,

Thanks for trying out Clair3. For us to pinpoint the problem, could you send the running log ${OUTPUT_DIR}/run_clair3.log and the log directory ${OUTPUT_DIR}/log to zxzheng@cs.hku.hk?

BTW, were you using the most recently released v0.1-r3 version?

[agos316]

Zheng,

It is no problem, the clair software works great for my application. let me gather the files and send them. Additionally, yes I am using v0.1-r3

Best

[zhengzhenxian]

Hi, Marc,

Thanks for sending over your log, we confirmed it is a bug in Clair3 that will be triggered when candidate variants are too few. We updated the code with a boundary check (preprocess/SelectQual.py line 52 and line 70, preprocess/SelectCandidates.py line 234). The fix will be included in r4 that will be rollout by the end of June.

[agos316]

Look forward to the update. Thanks for your help.

[aquaskyline]

fixed in v0.1-r4