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alachins / raisd

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors
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Duplicate windows variable statistic values #17

Closed silastittes closed 4 years ago

silastittes commented 4 years ago

Hello, Thanks for your work! I noticed that some windows are repeated in my analysis. Here's an example:

272909792       272908832       272910752       1.210e-01       1.032e+00       2.156e+00       2.693e-01
272909792       272908832       272910752       1.210e-01       1.032e+00       2.197e+00       2.744e-01
272909792       272908832       272910752       1.210e-01       1.032e+00       2.197e+00       2.744e-01
272909792       272908832       272910752       1.210e-01       1.032e+00       2.243e+00       2.801e-01
272909792       272908832       272910752       1.210e-01       1.032e+00       2.232e+00       2.787e-01
272909792       272908832       272910752       1.210e-01       1.032e+00       1.898e+00       2.370e-01
272909792       272908832       272910752       1.210e-01       1.032e+00       1.948e+00       2.432e-01

Is this behavior expected? Thank you!

alachins commented 4 years ago

Can you check whether there are multiple SNPs at the same position in your dataset? I can look into that if you sent me a small sample of your file that reproduces this behavior.

silastittes commented 4 years ago

Here's the input and output files needed to reproduce the behavior.

Thanks for looking in to this!

command: raisd-master/RAiSD -R -s -m 0.05 -n LR_dup2 -I SNPs_only.recode.vcf -S LR_Crucero_Lagunitas_IDkey.txt -f

(note, I've appended .txt so GitHub would upload). RAiSD_Info.LR_dup2.txt RAiSD_Report.LR_dup2.1.txt SNPs_only.recode.vcf.txt LR_Crucero_Lagunitas_IDkey.txt

alachins commented 4 years ago

I just pushed version 2.5 that fixes this. There was a bug (due to typecasting) that was causing some site positions to be off by 1 bp when stored in memory. Can you please try v2.5 on your full dataset and let me know?

Thank you very much for reporting this.

silastittes commented 4 years ago

I'm not seeing any duplicate windows with the update! I've closed the issue. Thank you!