Javascript read depth and random sampling on bai (bam) and tba (vcf/tabix) index file and binary readers

function estimateCoverageDepth (indexReader, cb)

An estimator of coverage depth of corresponding data file (for the index reader - bam or vcf) which uses bytes in region segments as the indicator. Returns the estimations as a map M of vectors of 'segment information' maps, where each key in M is a reference id and each corresponding value is a vector [seg-info-map, ...] of maps which each map is

{relBinNum: (segment-bin-num - start16kbBinid),
 pos: (relBinNum * 16KB),
 depth: total-byte-count}

The estimate of coverage depth is based on the number of bytes within a chunk of the file. This is computed by taking all the leaf bins (the bins which cover 16kb regions, ranging from binid 4681 to 37449), taking the chunks they contain (any actual data within their 16kb region) and summing the total byte count. The relBinNum is a leaf bin ordinal value relative to start16kbBinid = 4681. Pos then is this ordinal times 16kb = byte offset of 16kb region. Depth is the total byte count in chunk.

function mapSegCoverage (indexReader, refid, fn, keepNils) {

Mapping function over the estimate read coverage segments of reference REFID. See estimateCoverageDepth for more on segments. Requires that estimateCoverageDepth has been run; if not will implicitly run it. FN is a function of a segment information map. For the sq of segment information maps for REFID [segmap...], returns the sq [fn(seqmap)...]. If keepNils is true, returns fn results which are nil (undefined), otherwise, returns only non nil results.

function samplingRegions (refs, options) {

For a sq of reference objects REFS (as obtained from file header information), and option set OPTIONS (a map of parameter options), obtains a set of region samples for each reference in refs. The resulting set is intended to be a 'representative sample' of the base file.

Tuning parameters in options are binSize, the max size covered by a bin; binNumber, the max number of bins to consider for a ref; start, the starting position of the sequence associated with a ref for a sampling. Defaults are binSize = 40000 bases, binNumber = 20, start = 1.

Returns a map {regions: [reginfo...], regstr: json-string-for-regions}

where reginfo = {name: ref.name, start: int, end: int} and regions is sorted ascendingly by name by numerical start

function new2oldRefs (refs) {

Convert ref objects to old format. Servers should be upgraded to use the actual bai index names, but this will provide interim support. Takes a sq REFS of reference objs, each of format {name: string, l_ref: int, l_name: int} and converts to sq of objs of format {name: string, end: int}

function bamStatsAliveSamplingURL (refs, options, bsaliveURL) {

Obtain a bamstats-alive url encoding for a region sampling of REFS a sq of reference objects as obtained from file header information. Performs a samplingRegions operation to obtain the region information and then generates a corresponding url for the bamstats-alive server. OPTIONS is as for samplingRegions. bsaliveURL is the base http address for a bamstats-alive server.