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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Correct handling on single description in paired end reads in exportReadsForClones #103

Closed dbolotin closed 8 years ago

dbolotin commented 8 years ago

Here: https://github.com/milaboratory/mixcr/blob/develop/src/main/java/com/milaboratory/mixcr/cli/ActionExportCloneReads.java#L149

Something like this: https://github.com/milaboratory/mixcr/blob/develop/src/main/java/com/milaboratory/mixcr/cli/ActionExportReads.java#L89

PoslavskySV commented 8 years ago

When this is possible (1 description but 2 reads)? All should be ok now since createRead always called using createRead(vdjca.getOriginalSequences(), vdjca.getDescriptions())

dbolotin commented 8 years ago

Actually just for comparison with some intermediate MiXCR versions with the following lines of code: https://github.com/milaboratory/mixcr/blob/4887d2a2d1d8128e350060b5214dc4e5cefab447/src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java#L200

And to make this part a bit more robust, in case we will decide to change something about read description.