getPL Returning Incorrect Values

[hakanEdico]

When using the getPL() function from genotype.java, I am getting incorrect values returned.
For example in this VCF line:

GL000206.1 6870 . C T 11.04 . AC=1;AF=0.500;AN=2;DP=16;FS=6.990;MQ=39.29;MQRankSum=-1.036;QD=0.69;ReadPosRankSum=-2.383;SOR=3.258;FractionInformativeReads=0.625;R2_5P_bias=31.099 GT:AD:AF:DP:GQ:PL:GL:GP:PRI:SB:MB 0/1:6,4:0.400:10:45:45,0,50:-4.55,0.00,-5.00:7.864e-02,9.214e-01,4.618e-06:0.00,34.77,37.77:3,3,0,4:4,2,1,3

Where the PL is "45,0,50"
The getPL() function returns [0, 46, 50]

Its always the second highest value incremented by one... very weird.

I am running on centos6/7
Version 2.0.1

EDIT: GL,GP,PRI were added recently, when they are removed this problem does not occur.

[yfarjoun]

Observation: Your GP and PL are inconsistent. According to the GP you have [-4.55,0.00,-5.00] which would imply PL= [46, 0, 50], but you PL is [45, 0, 50]. I agree that this is a bug.. it seem to stem from htsjdk/variant/vcf/AbstractVCFCodec.java:721 where the PL *derived* from your GL overwrites the PL. I'll submit a PR for this shortly. Thanks!!

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On Tue, Mar 6, 2018 at 8:44 PM, hakanEdico ***@***.***> wrote: When using the getPL() function from genotype.java, I am getting incorrect values returned. For example in this VCF line: GL000206.1 6870 . C T 11.04 . AC=1;AF=0.500;AN=2;DP=16;FS=6. 990;MQ=39.29;MQRankSum=-1.036;QD=0.69;ReadPosRankSum=-2.383;SOR=3.258; FractionInformativeReads=0.625;R2_5P_bias=31.099 GT:AD:AF:DP:GQ:PL:GL:GP:PRI:SB:MB 0/1:6,4:0.400:10:45:45,0,50:- 4.55,0.00,-5.00:7.864e-02,9.214e-01,4.618e-06:0.00,34.77, 37.77:3,3,0,4:4,2,1,3 Where the PL is "45,0,50" The getPL() function returns [0, 46, 50] Its always the second highest value incremented by one... very weird. I am running on centos6/7 Version 2.0.1 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1097>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACnk0r6nPdjus-egqfcWHJlalMXobbeqks5tbzt5gaJpZM4SfufW> .

[yfarjoun]

I submitted a PR #1098 that fixes this issue and I used the VariantContext that you supplied. please let me know if that it not OK.

[hakanEdico]

I have downloaded/compiled your branch and the issue is still present for me.

EDIT: Might've compiled the wrong branch! Let me retry.

[hakanEdico]

The fix works, thanks a lot!

One unrelated question, in the past our project has used
LineReaderUtil.fromBufferedStream(vcfIstream) where vcfIstream is a FileInputStream object.

Looks like that is deprecated now, is it safe to use
AsciiLineReader.from(vcfIstream) instead?

EDIT: Getting this warning:
AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream

What should I be using instead? BufferedLineReader?

Problem is the next line is
LineIteratorImpl iterator = new LineIteratorImpl(reader)
And BufferedLineReader cannot be converted to LineReader

EDIT2:

SynchronousLineReader reader = new SynchronousLineReader(vcfIstream);
LineIteratorImpl iterator = new LineIteratorImpl(reader);

Seems to work

[yfarjoun]

Please open a new issue for unrelated issues.