Why is getChr deprecated?

[jrobinso]

I get zillions of these warnings when compiling IGV

Warning:(241, 46) java: getChr() in htsjdk.tribble.Feature has been deprecated

Really, why is this neccessary? I'm not going to change all these to getContig. I realize not every sequence is a chromosome but not every sequence is a contig either. I know this is old news but am raising it now in hopes that you would consider removing the @deprecated tag. As the creator of tribble, maybe you can give me a break here?

[nh13]

For background: #197

[tfenne]

I'm sorta with Jim here. I'd be more on-board with the deprecation if we'd gone with getRefName or similar, but as Jim points out contig is just as incorrect as chr - moreso if you consider that most of the time folks are aligning to genomes containing chromosomes that are scaffolds not contigs! @lbergelson & @jacarey thoughts?

[jrobinso]

Why not just leave it as is and have them be synonyms? i.e. just remove @deprecated.

[jrobinso]

The problem I currently have is finding true deprecations in this sea of getChr warnings.

[lbergelson]

We wanted to encourage a single method name over a large variety of different similar method names by deprecating all but one of them. I understand that getContig may not be the ideal name. I believe we've settled on getRefName for htsjdk3. I'd prefer to not have 2 un-deprecated versions though since it leads to confusion.

I've opened a PR igvteam/igv#590 to migrate igv to getContig. Maybe that can solve the problem?

[jrobinso]

OK, thanks for the PR but I will wait for getRefName

[jrobinso]

IGV has a very large user base of its source code I'm not going to confuse everyone with a massive change to getContig. I will consider using getRefName when that is the name.

[magicDGS]

I believe we've settled on getRefName for htsjdk3

Indeed, for htsjdk3 it will be getRefName (see samtools/htsjdk-next-beta#6)
Maybe an idea is to make the same change in htsjdk2 with deprecation of getChr to make possible to migrate to htsjdk3 smoothly (and also, making possible to update IGV accordingly).