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1. Commits on Nov 21, 2014

   • Check for missing variant in MultipleVariantIterator - important if one

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2. Commits on Nov 14, 2014

   • SyncedVariantIterator now outputs "sparse" Variant vectors

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     jmthibault79

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3. Commits on Nov 7, 2014

   • Diversify the ref bases for a slightly better test

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4. Commits on Nov 4, 2014

   • 1. Modified ReferenceBlockSplittingVariantIterator to insert 'N' as the

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   • ReferenceBlockSplittingVariantIterator

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     jmthibault79

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5. Commits on Oct 30, 2014

   • Handle file/index not found errors in reader classes gracefully instead of segfaulting!

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     droazen

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6. Commits on Oct 27, 2014

   • Merge pull request #319 from broadinstitute/dr_variant_builder

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     droazen

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7. Commits on Oct 24, 2014

   • VariantBuilder: high-performance creation of Variant records

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     droazen

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8. Commits on Oct 21, 2014

   • Store all variant headers and also combine them for an overall header

     

     jmthibault79

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     kgururaj

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9. Commits on Oct 16, 2014

   • 1. Modified SharedFieldIterator and IndividualFieldValueIterator to

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     kgururaj

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10. Commits on Oct 3, 2014

    • Fix handling of vector end values by Genotype::operator[]

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      droazen

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11. Commits on Oct 2, 2014

    • Merge variant headers

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      jmthibault79

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12. Commits on Sep 24, 2014

    • Merge pull request #258 from broadinstitute/intel_int_cast_missing_end_fix

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      Mauricio Carneiro

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    • Multiple line sequence for reference testing

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13. Commits on Sep 23, 2014

    • Modified convert_data_to_integer and convert_data_to_float so that vector_end and missing values

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      kgururaj

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14. Commits on Sep 22, 2014

    • Add ReferenceIterator class: loads one chromosome at a time

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      jmthibault79

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    • Move ReferenceMap from foghorn: loads whole reference into memory

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15. Commits on Sep 2, 2014

    • Add .vcf.gz test to VariantReader/Iterator and MultipleVariantReader/Iterator

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16. Commits on Aug 29, 2014

    • updating hom_ref and hom_var to work with alternate ploidies

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      lbergelson

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17. Commits on Aug 28, 2014

    • Added non_ref_het() returning true only if it is a het() and none of the alleles is the reference (key == 0)

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      kshakir

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18. Commits on Aug 22, 2014

    • Add a test for input files with different variants

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      jmthibault79

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    • Add test for MultipleVariantReader GVCF and GBCF

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19. Commits on Aug 21, 2014

    • Merge pull request #200 from broadinstitute/mc_interval_support_163

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      MauricioCarneiro

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    • Sam: implementation of mate operations

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      Mauricio Carneiro

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    • Interval: add interval parsing support

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      Mauricio Carneiro

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    • IndexedVariantReader/Iterator

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      jmthibault79

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20. Commits on Aug 20, 2014

    • Indexed iteration of bam/cram files. #7

      kshakir

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21. Commits on Aug 14, 2014

    • Add Variant::alignment_stop() accessor

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      jmthibault79

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22. Commits on Aug 9, 2014

    • Variant: refactor of the shared field api

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      Mauricio Carneiro

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23. Commits on Aug 6, 2014

    • VariantField: fix operator[] skip size

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      Mauricio Carneiro

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24. Commits on Aug 1, 2014

    • SamPairIterator: add testcase that has multiple secondary alignments in between the two primary alignments to test_paired.bam (and .sam)

      

      Mauricio Carneiro

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    • Variant: read api for format field strings

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      Mauricio Carneiro

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25. Commits on Jul 24, 2014

    • Variant: add id field getter

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      Mauricio Carneiro

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    • VariantReader: fix deallocated memory access

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      Mauricio Carneiro

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26. Commits on Jul 11, 2014

    • MultipleVariantReader and MultipleVariantIterator

      jmthibault79

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