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secondOfPair and firstOfPair flag is missing in the newest 0.18 adam transformed results from BAM #903

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dnaase opened this Issue Dec 23, 2015 · 1 comment

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dnaase commented Dec 23, 2015

Hi, i found that when i use the most recent 0.18 adam to transform bam file to adam, the secondOfPair and firstOfPair is missing, while the same bam file which i transformed use 0.17 adam, the secondOfPair and firstOfPair flag is still there.

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fnothaft Jan 7, 2016

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Hi @dnaase! We removed the firstOfPair and secondOfPair fields in bigdatagenomics/bdg-formats#52. These fields are replaced by readInFragment (see bigdatagenomics/bdg-formats#66). The goal of this change was to support sequencing technologies that generate more than 2 reads from a single fragment (e.g., Complete Genomics). readInFragment == 0 is the same as firstOfPair, while readInFragment == 1 is the same as secondOfPair. Let me know if you've got any more questions!

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fnothaft commented Jan 7, 2016

Hi @dnaase! We removed the firstOfPair and secondOfPair fields in bigdatagenomics/bdg-formats#52. These fields are replaced by readInFragment (see bigdatagenomics/bdg-formats#66). The goal of this change was to support sequencing technologies that generate more than 2 reads from a single fragment (e.g., Complete Genomics). readInFragment == 0 is the same as firstOfPair, while readInFragment == 1 is the same as secondOfPair. Let me know if you've got any more questions!

@fnothaft fnothaft closed this Jan 12, 2016

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