deleting SAMFileReader and SAMTruncatedFileReader

[lbergelson]

Description

The long deprecated SAMFileReader and SAMTruncatedFileReader were supposed to be deleted in #602. They seem to have been resurrected during the move to gradle.

Fixes #695

renamed SAMFileReaderTest to the more accurate SamReaderTest
updated usages of SAMFileReader in the documentation to be SamReader

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[coveralls]

Coverage increased (+0.5%) to 69.397% when pulling 92d8382 on lb_redelete_deprecated_reader into c3d5a88 on master.

[droazen]

Can you check to make sure these classes are not used in either Picard or GATK3?

[lbergelson]

@droazen Both Picard and GATK3 make use of them. How to proceed?

[droazen]

@lbergelson Recommend that we open PRs (or at least, issues) against Picard and GATK3 to remove the usages before merging this.

[lbergelson]

@droazen Opened issues and rebased this. Should we wait for them to be resolved or merge this before that happens?

[coveralls]

Coverage increased (+0.5%) to 69.458% when pulling a0e259f on lb_redelete_deprecated_reader into 255e41a on master.

[droazen]

@lbergelson I'd say wait until the Picard one is merged, since it's simple, but don't wait for GATK3.

[lbergelson]

Uses were removed from both GATK and Picard so I'm going to merge this.