All.joiner problem

There is a problem with all.joiner rules and the -database parameter. This is taken from an email from Ann in 2007:

Bob and I just ran into something sneaky with running joinerCheck or runJoiner.csh. There are some rules that can be tricky and we are not exactly sure why. What we do know is the kind of output you can be on the lookout for to know that you're dealing with a "tricky" rule. The output sort of makes it look like the rule has run (with no problems), but it really hasn't run at all.

Example of rules that aren't really running from joinerCheck:

[hgwdev:~/joiner> joinerCheck -keys -database=fr2 -identifier=blastHg18KGPep04Id all.joiner
Checking keys on database fr2

from runJoiner.csh:

[hgwdev:~/joiner> runJoiner.csh fr2 blastHg18KG
found identifiers:

blastHg18KGRef04Id
blastHg18KGPep04Id

Checking keys on database fr2
Checking keys on database fr2

If the rule had really run there would be some output saying something like X hits out of Y ok.

The way to force these rules to run is to leave off the "database" parameter (you can only do this when using the joinerCheck (runJoiner.csh can't handle that)). This will run the rule for all databases that are listed -- just pick yours out of the output.

[hgwdev:~/joiner> joinerCheck -keys -identifier=blastHg18KGPep04Id all.joiner Checking keys on database (null)
 anoCar1.blastHg18KG.qName - hits 45332 of 45332 ok
 equCab1.blastHg18KG.qName - hits 61628 of 61628 ok
 ornAna1.blastHg18KG.qName - hits 35761 of 35761 ok
 oryLat1.blastHg18KG.qName - hits 38111 of 38111 ok
 bosTau2.blastHg18KG.qName - hits 56832 of 56832 ok
 strPur1.blastHg18KG.qName - hits 30907 of 30907 ok
 mm8.blastHg18KG.qName - hits 70754 of 70754 ok
 fr2.blastHg18KG.qName - hits 40510 of 40510 ok 
 dm2.blastHg18KG.qName - hits 22239 of 22239 ok
 felCat3.blastHg18KG.qName - hits 37715 of 37715 ok
 canFam2.blastHg18KG.qName - hits 62741 of 62741 ok
 danRer4.blastHg18KG.qName - hits 44692 of 44692 ok
 xenTro2.blastHg18KG.qName - hits 40291 of 40291 ok
 galGal3.blastHg18KG.qName - hits 35851 of 35851 ok
 monDom4.blastHg18KG.qName - hits 63264 of 63264 ok
 hg18.blastKGRef04.acc - hits 36727 of 36727 ok
 hg18.knownGene.name - hits 0 of 56722
Error: 56722 of 56722 elements of hg18.knownGene.name are not in key blastKGPep04.name line 1995 of all.joiner
Example miss: UC001AAA.1