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[ADAM-1393] fix missing reads when transforming fastq to adam #1394

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merged 1 commit into from Feb 21, 2017

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@A-Tsai
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A-Tsai commented Feb 17, 2017

To fix #1393, don't double count the length of the readname line. In addition, to prevent the length of a line is longer than MAX_LINE_LENGTH in https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java#L330

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AmplabJenkins Feb 17, 2017

Can one of the admins verify this patch?

Can one of the admins verify this patch?

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heuermh Feb 17, 2017

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@A-Tsai thank you for the help on this issue!

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heuermh commented Feb 17, 2017

@A-Tsai thank you for the help on this issue!

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Jenkins, test this please

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heuermh commented Feb 17, 2017

Jenkins, test this please

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AmplabJenkins Feb 17, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1805/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1805/
Test PASSed.

@fnothaft

Thanks @A-Tsai! I will leave this open until next week for others to review, but it looks great from my side. We greatly appreciate you contributing a fix!

@heuermh heuermh changed the title from fix missing reads when transforming fastq to adam to [ADAM-1393] fix missing reads when transforming fastq to adam Feb 21, 2017

@heuermh heuermh merged commit 0e57357 into bigdatagenomics:master Feb 21, 2017

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Thank you, @A-Tsai!

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heuermh commented Feb 21, 2017

Thank you, @A-Tsai!

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