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Commits on May 19, 2018

• Add option to downsample input alignments (--downsampling-rate).

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  9cd384a

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Commits on Apr 3, 2018

• Write reference ids of the chromosomes to the sbip file.

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Commits on Jan 23, 2018

• Make test of example id conditional (the set can grow very large with million of examples and this would slow loading considerably).

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  d54261b

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Commits on Jan 18, 2018

• Use flap to calculate first position to skipTo. This fixes a bug that skipped reads at the beginning of a slice.

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  f3c231b

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Commits on Jan 8, 2018

• Update change log.

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  1ec163f

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• Make a copy of the readers with more entries so that the loop cannot modify it. This fixes the concat bug which created an empty alignment when many empty alignments preceeded parts with content.

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  6131f8c

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• Make SAM reader silent. Too many errors reported on the console when reading.

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  13629af

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Commits on Dec 15, 2017

• Fix bound.

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  7088d06

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• Add a test with from length different from alt length.

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  773b9f5

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• Handle potential case when form and alts are not the same length. How does this happen?

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  8ca1e03

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• Add a test to demonstrate the problem we discussed in lab meeting,

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Commits on Nov 15, 2017

• Remove varmap.

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  231ae16

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• Prevent possible NPE when no records are written.

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  bde2349

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• Advance to next snapshot.

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  2a549ef

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Commits on Nov 14, 2017

• Add state of the art genotyping model as new default.

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  ed02da0

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• Updated change log for new release.

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  bd8a676

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Commits on Nov 9, 2017

• Another reorganization attempt to improve speed and memory consumption while preserving correct behavior.

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  3217882

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• Revert to previous commit, which did improve indel performance by removing duplicates. Complete refactoring resulted in a doubling of the number of sites output. Need to investigate more since the …

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Commits on Nov 8, 2017

• Simplify handling of bases and flushing to output format.

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  90e68bc

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• Eliminate duplicate records around indels.

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  ecaf26f

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Commits on Nov 3, 2017

• Changes to support one offset per count, not just one per sample.

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  37b25f1

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Commits on Nov 2, 2017

• Add fields to keep track of true genotype before post-processing as well as offset.

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  a7f1c8a

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Commits on Oct 27, 2017

• Need to reintroduce synchronized here. I got NPEs due to synchronization errors when runing in parallel.

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  086cebd

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• Fix field id.

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  758274e

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• Add true genotype field on sample.

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  91ed6ae

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Commits on Oct 26, 2017

• Add reference allele and formatted count on base.

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  5e6205c

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• Try catch IOException inside flush (less frequent).

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• Handle statistics inside the writer.

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  8ab2f6d

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Commits on Oct 23, 2017

• Add isVariant attribute to the base.

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  0bb48e6

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• Extension was previously correct, this is the sbi reader.

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  17784e9

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• Correct bool type and add color attribute to base.

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  e24a3cf

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• Add information about indel to Base message.

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  27760c3

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Commits on Oct 18, 2017

• Fix property for number of segments.

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  4845517

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• Fix the extension again: it is .ssi for segments.

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  738370a

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• Emulate property keys used by feature mapper when reading .ssip file.

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