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Index stats estimation #1167

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merged 9 commits into from Aug 13, 2018

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cmdcolin commented Aug 10, 2018

This is a PR to address #1092

It performs a simplified stats estimation that is based on getting feature counts from the index. Then it estimates feature density simply as feature count divided by length of chromosome. CSI, BAI, and Tabix all have this ability. CRAI index actually does not have feature count in its index.

The command samtools idxstats can demonstrate this function and outputs feature counts, and on CRAI it does a slower calculation that is not implemented in this PR, so CRAM falls back to global stats estimation samtools/samtools#832

Might be worth ignoring whitespace using https://github.com/GMOD/jbrowse/compare/dev...index_stats_estimation?w=1 on this PR as some of the whitespace in these files was wonky

cmdcolin added some commits Aug 10, 2018

}
return 0;
},

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@rbuels

rbuels Aug 13, 2018

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come on bro, use modern let and const

@rbuels

rbuels Aug 13, 2018

Collaborator

come on bro, use modern let and const

intBins[intBinsL[i]] = true;
}
return intBins;
}.call(this);

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@rbuels

rbuels Aug 13, 2018

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no, use a regular block context or something. no more function() {}.call(this) to get block scoping.

@rbuels

rbuels Aug 13, 2018

Collaborator

no, use a regular block context or something. no more function() {}.call(this) to get block scoping.

@rbuels rbuels merged commit e702fa9 into dev Aug 13, 2018

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@wafflebot wafflebot bot removed the in progress label Aug 13, 2018

@rbuels rbuels added this to the 1.15.2 milestone Aug 13, 2018

@cmdcolin cmdcolin deleted the index_stats_estimation branch Aug 14, 2018

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