Bam file indexes being removed

[mattloose]

We try and clean up files at all times. At some point we are removing the index for the input bam file.

This needs to be resolved and left untouched.

[mattloose]

Error possibly tracked to coverage

[mattloose]

Coverage error fixed. Additional error in classifier where it tried to delete afile that doesn't exist.

[mattloose]

Need to check each sub function and main class.

• [x] main code
• [x] sturgeon
• [x] nanodx
• [x] forest
• [x] cnv
• [x] mgmt
• [x] fusion
• [x] coverage

[mattloose]

Fusion code was leaving residual csi files.