Code style and doc fixes

[heuermh]

Fixes #100

Binary incompatible code changes are described by the clirr plugin:

$ mvn clirr:check
...
[INFO] --- clirr-maven-plugin:2.6.1:check (default-cli) @ bdg-formats ---
[INFO] Comparing to version: 0.9.0
[ERROR] 8001: o.b.f.avro.Base: Class org.bdgenomics.formats.avro.Base removed
[ERROR] 6001: o.b.f.avro.Feature: Removed field isCircular
[ERROR] 7002: o.b.f.avro.Feature: Method 'public java.lang.Boolean getIsCircular()' has been removed
[ERROR] 7002: o.b.f.avro.Feature: Method 'public void setIsCircular(java.lang.Boolean)' has been removed
[ERROR] 7002: o.b.f.avro.Feature$Builder: Method 'public org.bdgenomics.formats.avro.Feature$Builder clearIsCircular()' has been removed
[ERROR] 7002: o.b.f.avro.Feature$Builder: Method 'public java.lang.Boolean getIsCircular()' has been removed
[ERROR] 7002: o.b.f.avro.Feature$Builder: Method 'public boolean hasIsCircular()' has been removed
[ERROR] 7002: o.b.f.avro.Feature$Builder: Method 'public org.bdgenomics.formats.avro.Feature$Builder setIsCircular(java.lang.Boolean)' has been removed
[ERROR] 6001: o.b.f.avro.Genotype: Removed field isPhased
[ERROR] 7002: o.b.f.avro.Genotype: Method 'public java.lang.Boolean getIsPhased()' has been removed
[ERROR] 7002: o.b.f.avro.Genotype: Method 'public void setIsPhased(java.lang.Boolean)' has been removed
[ERROR] 7002: o.b.f.avro.Genotype$Builder: Method 'public org.bdgenomics.formats.avro.Genotype$Builder clearIsPhased()' has been removed
[ERROR] 7002: o.b.f.avro.Genotype$Builder: Method 'public java.lang.Boolean getIsPhased()' has been removed
[ERROR] 7002: o.b.f.avro.Genotype$Builder: Method 'public boolean hasIsPhased()' has been removed
[ERROR] 7002: o.b.f.avro.Genotype$Builder: Method 'public org.bdgenomics.formats.avro.Genotype$Builder setIsPhased(java.lang.Boolean)' has been removed
[ERROR] 6001: o.b.f.avro.GenotypeAllele: Removed field Alt
[ERROR] 6001: o.b.f.avro.GenotypeAllele: Removed field NoCall
[ERROR] 6001: o.b.f.avro.GenotypeAllele: Removed field OtherAlt
[ERROR] 6001: o.b.f.avro.GenotypeAllele: Removed field Ref
[ERROR] 6001: o.b.f.avro.Variant: Removed field isSomatic
[ERROR] 7002: o.b.f.avro.Variant: Method 'public java.lang.Boolean getIsSomatic()' has been removed
[ERROR] 7002: o.b.f.avro.Variant: Method 'public void setIsSomatic(java.lang.Boolean)' has been removed
[ERROR] 7002: o.b.f.avro.Variant$Builder: Method 'public org.bdgenomics.formats.avro.Variant$Builder clearIsSomatic()' has been removed
[ERROR] 7002: o.b.f.avro.Variant$Builder: Method 'public java.lang.Boolean getIsSomatic()' has been removed
[ERROR] 7002: o.b.f.avro.Variant$Builder: Method 'public boolean hasIsSomatic()' has been removed
[ERROR] 7002: o.b.f.avro.Variant$Builder: Method 'public org.bdgenomics.formats.avro.Variant$Builder setIsSomatic(java.lang.Boolean)' has been removed

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/119/
Test PASSed.

[jpdna]

+1

[fnothaft]

LGTM!

[fnothaft]

Merged! Thanks @heuermh !

[heuermh]

Thanks!