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Bug in SNP GUI code #83

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Merged
standage merged 2 commits into from
Apr 24, 2025
Merged

Bug in SNP GUI code #83

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da03845
fixed bug in GUI
rnmitchell Apr 23, 2025
b28636c
added detection threshold of 10
rnmitchell Apr 23, 2025
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8 changes: 4 additions & 4 deletions lusSTR/cli/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -922,8 +922,8 @@ def show_SNP_page():

clicked_wd = col1.button("Please Select An Output Folder")
if clicked_wd:
wd = folder_picker_dialog()
st.session_state.wd_dirname = wd
wd_dirname = folder_picker_dialog()
st.session_state.wd_dirname = wd_dirname

# Display selected path
if st.session_state.wd_dirname:
Expand All @@ -937,7 +937,7 @@ def show_SNP_page():
if st.button("Submit"):

# Check if all required fields are filled
if analysis_software and samp_input and output and wd_dirname:
if analysis_software and samp_input and output and st.session_state.wd_dirname:

# Validate output prefix
if not validate_prefix(output):
Expand Down Expand Up @@ -976,7 +976,7 @@ def show_SNP_page():
command = ["lusstr", "snps", "all"]

# Specify WD to lusSTR
if wd_dirname:
if st.session_state.wd_dirname:
command.extend(["-w", st.session_state.wd_dirname + "/"])

# Run lusSTR command in terminal
Expand Down
2 changes: 1 addition & 1 deletion lusSTR/wrappers/snps_convert.py
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Expand Up @@ -158,7 +158,7 @@ def straitrazor_filtering(sr_df, thresh):
if sr_df.loc[i, "Issues"] == "Allele call does not match expected allele!":
sr_df = sr_df.drop(i)
else:
if allele_reads < (total_snp_reads * thresh):
if allele_reads < (total_snp_reads * thresh) or allele_reads < 11:
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@rnmitchell rnmitchell Apr 23, 2025

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Added a detection threshold of 10

sr_df.loc[i, "Reads"] = 0
return sr_df

Expand Down