SamSequenceDictionaryExtractor for cram

[lindenb]

Description

I'm currently working on a "Reference registry" that would allow to find the path to a fasta REF for a given sequence dictionary.

I wish it works on cram but SAMSequenceDictionaryExtractor currently doesn't handle the CRAM format. This PR adds the support for CRAM.

overview

In CRAMIterator I wrote a static method extractDictionaryto open a CRAM file without a CRAMReferenceSource (well, a fake one that shouldn't be called) to only get the CRAM header+dict

In SAMSequenceDictionaryExtractor.java I added a new enum for CRAM that calls CRAMIterator.extractDictionary

I also added two test files: toy.cram and toy.dict

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)

[codecov-io]

Codecov Report

Merging #1305 into master will decrease coverage by 0.002%.
The diff coverage is 70%.

@@               Coverage Diff               @@
##              master     #1305       +/-   ##
===============================================
- Coverage     67.644%   67.642%   -0.002%     
- Complexity      8188      8189        +1     
===============================================
  Files            560       560               
  Lines          33462     33472       +10     
  Branches        5635      5635               
===============================================
+ Hits           22635     22641        +6     
- Misses          8644      8648        +4     
  Partials        2183      2183

Impacted Files	Coverage Δ	Complexity Δ
.../variant/utils/SAMSequenceDictionaryExtractor.java	73.171% <100%> (-1.188%)	1 <0> (-1)
src/main/java/htsjdk/samtools/CRAMIterator.java	80.282% <62.5%> (-1.062%)	34 <2> (+2)

[lbergelson]

This looks good to me. Very logical extension of the existing utility. Thank you @lindenb