Add -a,--all option to cmpbams so it compares all reads

[lckarssen]

Description

This commit adds the -a,--all option to cmpbams. When this option is set, cmpbams will also compare reads marked as supplementary or secondary.

This fixes #151.

Checklist

• [x] Code compiles correctly
• [x] All tests passing
• [x] Extended the README / documentation, if necessary
• [ ] Added myself + history to the source file

[lckarssen]

Regarding the last point in the checklist: I'm willing to add my name, but given that it is such a small change, I'm not sure if it is necessary.

[lindenb]

Thanks !