[~aloraine], I have tried to build IGB project after removing these legacy maven repos from the POM.
Build was failing for affymetrix common and was asking for missing dependency jlgfr. I commented it from the POM and it was built successfully.
After that, it was failing for genometry module because com.affymetrix:fusion dependency. It is being used in the module and its not there in nexus.bioviz.org.
Please let me know if there is any other repository location which can be referred in the POM?

For the next steps, can you do this?

• investigate "affymetrix fusion" - where is the source code? What packages/classes are being used, and where? We may be able to eliminate it. (If the source code is not available, we should write it out of the project.)
• investigate: what is jlgfr ? Same as above.

Feel free to make these tasks two new Jira tickets - as you see fit.

affymetrix fusion -
1) Its is being used in two files under genometry module.
comaprator/QuantByIntIdComparator
comparator/QuantDetectByIntIdComparator
package used : affymetrix.calvin.data
2)The source code is present at :
https://github.com/HenrikBengtsson/Affx-Fusion-SDK/tree/master/affy/sdk/java/AffxFusion

jlfgr-
I am not able to locate the source code but it has something to do with the icons in IGB.
Its a java look and feel Graphics repository dependency.
Also, in the NOTICES.txt file it is mentioned that " IGB can be used with or without this jar file.".
So, I am not sure if that is necessary.

Changing scope of this ticket: please remove reference to AffxFusion jar on a topic branch named for this Jira ticket - IGBF-1948.

We will remove the other dependencies as part of other Jira issues.

Prof. [~aloraine], I have removed AffxFusion dependency from everywhere except igb module.
It used in the "ChpParser" file of the Parsers directory of igb module which is used in "getGenome" function of "QuickLoadSymLoaderChp" class. This getGenome function is used almost everywhere in IGB codebase. I am not sure if we can remove this dependency.

Thanks Prutha Kulkarni!

For the next step, can you do this?

Add a new comment that all functions coming from the AffxFusion artifact that are used in IGB code base?

Please list:

• function name - name of function in AffxFusion
• class name - class where the function is implemented
• package - package (in AffxFusion) where the class resides

When done, move this to Needs First Level Review.

package is common for all which is "affymetrix.fusion.chp"
List of classes and function used is given below:
1) class: FusionCHPData
function name: getHeader, getExpressionResults
2) class: FusionCHPDataReg
function name: read
3) class: FusionCHPGenericData
function name: fromBase
4) class: FusionCHPHeader
function name: getAlgName, getAlgVersion, getAssayType, getChipType, getRows, getCols, getParentCellFile, getProgID, getNumProbeSets
5) class: FusionCHPLegacyData
function name: registerReader
6) class: FusionCHPQuantificationData
function name: registerReader
7) class: FusionCHPQuantificationDetectionData
function name: registerReader
8) class: FusionCHPTilingData
function name: registerReader
9) class: FusionExpressionProbeSetResults
function name: getDetectionPValue, getSignal, clear

Use of affx jar is documented above. Moving to Closed.