move protocol s3 from qio to qpicard #226
Conversation
|
s3 package should stay in qio as it is to do with input and output. Let me know when you have taken this out and I'll take another look - thanks |
| @@ -27,7 +27,7 @@ | |||
| import org.qcmg.common.log.QLogger; | |||
| import org.qcmg.common.log.QLoggerFactory; | |||
| import org.qcmg.common.string.StringUtils; | |||
| import org.qcmg.protocol.s3.S3AwareURLStreamHandlerFactory; | |||
| import org.qcmg.picard.s3.S3AwareURLStreamHandlerFactory; | |||
There was a problem hiding this comment.
I really don't understand this move. The s3 package is for low-level AWS operations - for example, all it ever throws is IOException. picard is specifically for handling fastq/bam/sam sequence data which is a way more specialized task. By moving this out of qio into qpicard that means any time I want to access ANY s3 file stream, whether it contains a VCF, text or whatever, I have to import a sequence data handling package. That just seems wrong to me.
A lot of my reluctance I think comes from my (very imperfect) understanding of what problem this is attempting to solve. It seems like if the issue is multiple paths to the same dependency, that is something that should be fixed in the build configuration (with excludes) rather than restructuring packages themselves.
Description
as described on #217
Fixes #217
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
existing unit test, whole gradle build and regression test
Checklist: