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Question : Why the number of paired sequence in adam-0.21.0 less than adam-0.19.0? #1424
I load fastq and count by :
fastq1 and fastq2 are 10000+10000=20000 sequences
I try to load fastq1 and fastq2:
the count are
Why both are not 10000?
Question : Why the number of paired sequence in adam-0.21.0 less than adam-0.19.0?
I can not find any err log information in IDEA(run in wondows 7):
The data is crested by wgsim tool (heng li: https://github.com/lh3/wgsim)
@heuermh I test small data with 6 paired-end reads, but loadAlignmnet only 5:
I test the native data in adam-0.21.0. the number of line in bqsr1-r1.fq is 1952, it should be 488 reads.
It should be total 976 reads after loadAlignments, but there are 892 reads by running my code.
I add the code into org.bdgenomics.adam.cli.Adam2FastqSuite
referenced this issue
Mar 8, 2017
Hmmm, interesting! I assume it was the
On the 0.21.0 tag, I do get dropped reads:
Can you try running on the latest master branch? I'm going to try to do a git bisect (or something of that type) to see if I can find the breaking change.
I test the latest master branch， there are correct in number.
Only Adam-0.21.0 and 0.20.0 have problem about it.
My project run with maven, I will try to replace old version with Adam jar. When the new version of Adam will release?
Thank you very much.
Hi @xubo245! I believe the error was fixed in 0e57357. We are planning to release ADAM 0.22.0 within the next two weeks (current slated date is 3/18); you can track our progress both here and on ticket #1210.
In the meantime, you can use the ADAM snapshot. A new snapshot gets built and pushed every time there is a commit to ADAM.