Make up to date with VertebrateResequencing / pbwt ? #50
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…h GATK allele depth
bugfix for reading and writing samples files
add a command -log to allow logging to a file
vcf/bcf opening can now do so via libcurl/irods if htslib configured for that
* ploidy I/O should now actually work * VCF output now treats missing data correctly * imputeMissing now called on the merge of the input data and frame prior to imputation * still some I/O work todo with missing/dosage and subsetting sites and samples
* add `-removeSamples` option * when subsetting samples and sites, also update `missing` for these subsets * fix bug in `pbwtRemoveSites` where it would not print out sites beyond the last site in the `removeSites` file * add tests
It was not practical. For a large input cohort most sites will have at least one sample with missing data and the given implementation would fall over
revert whitespace changes to clean up diff
rename `sample()` to `pbwtSample()` to indicate it is getting indexing into the `p->samples` array rather than the global `sampleDict`. `sample()` then is the used to look up in `sampleDict`.
reading the `.samples` file will now guess `isX` and `isY` by comparing the number of samples with the number of haplotypes. `pbwtReadVcfGT` requires the command line `-X` and `-Y` option to be set
not entirely sure what state this is in...
Because a static sample dictionary is used and two sample sets are read (once for input VCF and once for the reference panel), the sample indexes were incorrect.
Feature/ploidy
for the following command: valgrind ./pbwt -log /dev/null -readVcfGT test/refImpute.in.vcf -referenceImpute xxx/OMNI -writeVcf /dev/null
…eferenceImpute The kOld iterator is incremented before it is used, so the the >= equalities were selected incorrect (non-overlapping) segments. In this commit also matchSequencesSweepSparse() is replaced by matchSequencesSweep(), this may not be desired, not sure.
Test whether the assumption is true rather than inserting hard values to notify us about possible problems.
…g, correct order of updating cursor; in paintAncestryMatrix() free a couple more arrays to fix memory leak
…major allele [temporary solution]
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Gah... there's clearly too much here... Lets look at just the 13 commits in this fork that aren't in the VertebrateResequencing fork... |
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Hi Dan. Sorry, I just picked up this thread and will look at this. Richard
From: Dan Bolser ***@***.***>
Date: Tuesday, 8 March 2022 at 14:52
To: richarddurbin/pbwt ***@***.***>
Cc: Subscribed ***@***.***>
Subject: Re: [richarddurbin/pbwt] Make up to date with VertebrateResequencing / pbwt ? (PR #50)
Gah... there's clearly too much here... Lets look at just the 13 commits in this fork that aren't in the VertebrateResequencing fork...
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So... Looks OK... |
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Thanks so much, I got confused quite quickly trying to merge the two.
```
git rebase durbo/master
First, rewinding head to replay your work on top of it...
Applying: set htslib=1.2.1, pbwt=3.1 and link against bsd
Using index info to reconstruct a base tree...
A makefile
Falling back to patching base and 3-way merge...
CONFLICT (modify/delete): makefile deleted in HEAD and modified in set
htslib=1.2.1, pbwt=3.1 and link against bsd. Version set htslib=1.2.1,
pbwt=3.1 and link against bsd of makefile left in tree.
error: Failed to merge in the changes.
Patch failed at 0001 set htslib=1.2.1, pbwt=3.1 and link against bsd
hint: Use 'git am --show-current-patch' to see the failed patch
Resolve all conflicts manually, mark them as resolved with
"git add/rm <conflicted_files>", then run "git rebase --continue".
You can instead skip this commit: run "git rebase --skip".
To abort and get back to the state before "git rebase", run "git rebase
--abort".
```
…On Tue, 8 Mar 2022 at 15:03, Richard Durbin ***@***.***> wrote:
Hi Dan. Sorry, I just picked up this thread and will look at this. Richard
From: Dan Bolser ***@***.***>
Date: Tuesday, 8 March 2022 at 14:52
To: richarddurbin/pbwt ***@***.***>
Cc: Subscribed ***@***.***>
Subject: Re: [richarddurbin/pbwt] Make up to date with
VertebrateResequencing / pbwt ? (PR #50)
Gah... there's clearly too much here... Lets look at just the 13 commits
in this fork that aren't in the VertebrateResequencing fork...
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Perhaps it's my anal-retentive personality type, but the fact that you've diverged really bugs me.
If you don't want to merge changes, these should be separate projects no?
Cheers,