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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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ehh in Mac-arm version 2.0.3 doesn't work #120

Open alisi1989 opened 3 months ago

alisi1989 commented 3 months ago

Dear Spiezch, thank you for the new software release. I have a problem using version 2.0.3 for mac-arm version. the ihs nsl etc flags work fine, but the ehh flag doesn't work and says to use one and only one of the flags, see below. the same command I'm using with version 2.0.2 works normally instead. could it be a release problem? command: selscan-2.0.3 --ehh rs111111 --ehh-win 2000000 --vcf input.vcf.gz --map geneticmap.map --out test

selscan v2.0.3 ERROR: Must specify one and only one of EHH (--ehh) iHS (--ihs) XP-EHH (--xpehh) PI (--pi) nSL (--nsl) XP-nSL (--xpnsl) iHH12 (--ihh12)

thank you in advance for any suggestion

szpiech commented 3 months ago

Hi,

Sorry about this, I’ll look into it.

Zachary

Le lun. 22 juil. 2024 à 03:17, alisi1989 @.***> a écrit :

Dear Spiezch, thank you for the new software release. I have a problem using version 2.0.3 for mac-arm version. the ihs nsl etc flags work fine, but the ehh flag doesn't work and says to use one and only one of the flags, see below. the same command I'm using with version 2.0.2 works normally instead. could it be a release problem? command: selscan-2.0.3 --ehh rs111111 --ehh-win 2000000 --vcf input.vcf.gz --map geneticmap.map --out test

selscan v2.0.3 ERROR: Must specify one and only one of EHH (--ehh) iHS (--ihs) XP-EHH (--xpehh) PI (--pi) nSL (--nsl) XP-nSL (--xpnsl) iHH12 (--ihh12)

thank you in advance for any suggestion

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alisi1989 commented 3 months ago

thanks for the quick response. If it helps, I noticed that I also encounter the same problem on the Linux system with version 2.0.3.

szpiech commented 3 months ago

OK, thanks for catching that. Silly error on my part.

You can get the macos-arm version of 2.0.3a, which fixes this, here https://github.com/szpiech/selscan/blob/devel/bin/macos-arm/selscan-2.0.3a

I'll work on the linux version and merge it with the main branch soon.

Zachary

On Tue, Jul 23, 2024 at 1:46 AM alisi1989 @.***> wrote:

thanks for the quick response. If it helps, I noticed that I also encounter the same problem on the Linux system with version 2.0.3.

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alisi1989 commented 3 months ago

perfect thanks a lot. it works perfectly. just out of curiosity, I saw that in the example folder for the EHH there are also the .anc.colormap and .der.colormap output files, does this version also produce these outputs? Thanks again for the help and the software

szpiech commented 3 months ago

Hi,

I actually took those out in v2 (I think they were technically undocumented), but I’ve heard from some people that they were actually using them.

We’re doing a big re-write of the code, and I’ll make sure we get that re-implemented at that point. Sorry for that!

Zachary

Le mar. 23 juil. 2024 à 11:07, alisi1989 @.***> a écrit :

perfect thanks a lot. it works perfectly. just out of curiosity, I saw that in the example folder for the EHH there are also the .anc.colormap and .der.colormap output files, does this version also produce these outputs? Thanks again for the help and the software

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fish2022Jul commented 1 month ago

Hi, the 2.0.3 for linux is still not working....hope you can fix it soon. Thank you

szpiech commented 1 month ago

Hello,

Sorry for the issue. Would you please try v2.0.3a on the devel branch here https://github.com/szpiech/selscan/tree/devel/bin/linux

Zachary

On Fri, Oct 4, 2024 at 2:14 PM Peter Fu @.***> wrote:

Hi, the 2.0.3 for linux is still not working....hope you can fix it soon. Thank you

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