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BAM backend starting to work well, adapting @GreggHelt2 conversion co…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| define( ['dojo/_base/declare' | ||
| ], | ||
| function( declare ) { | ||
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| return declare( null, { | ||
| constructor: function( store, record ) { | ||
| var data = {}; | ||
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| // copy all of the fields verbatim to start, for things people might want | ||
| for( var k in record ) { | ||
| if( record.hasOwnProperty(k) ) | ||
| data['sam_'+k] = record[k]; | ||
| } | ||
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| // figure out start and end | ||
| data.start = data.sam_pos; | ||
| if( data.sam_lref ) { | ||
| data.end = data.sam_pos + data.sam_lref; | ||
| } else { | ||
| data.end = data.sam_pos + data.sam_seq.length; | ||
| } | ||
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| /* can extract "SEQ reverse complement" from bitwise flag, | ||
| * but that gives orientation of the _read sequence_ relative to the reference, | ||
| * whereas feat[STRAND] is intended to indicate orientation of the _template_ | ||
| * (in the case of RNA-Seq, the RNA that the read is derived from) relative to the reference | ||
| * for some BAM sources (such as TopHat), an optional field "XS" is used to to indicate RNA orientation | ||
| * relative to ref. 'XS' values are '+' or '-' (any others?), | ||
| * for some sources, lack of 'XS' is meant to indicate plus strand, only minus strand are specifically tagged | ||
| * for more on strandedness, see seqanswers.com/forums/showthread.php?t=9303 | ||
| * TODO: really need to determine whether to look at bitwise flag, or XS, or something else based | ||
| * on the origin of the BAM data (type of sequencer or program name, etc.) | ||
| * for now using XS based on honeybee BAM data | ||
| */ | ||
| // trying to determine orientation from 'XS' optional field | ||
| data.strand = data.sam_XS == '-' ? -1 : 1; | ||
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| data.score = data.sam_MQ; | ||
| data.type = 'match'; | ||
| data.source = store.source; | ||
| data.seq_id = data.sam_segment; | ||
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| data.name = data.sam_readName; | ||
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| this.data = data; | ||
| this.store = store; | ||
| this._uniqueID = data.name+':'+data.start+'..'+data.end; | ||
| }, | ||
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| // BamUtils.convertBamRecord = function (br, make_cigar_subfeats) { | ||
| // var feat = []; | ||
| // var arep = BamUtils.attrs; | ||
| // // var fields = this.fields; | ||
| // // feat[fields.start] = br.pos; | ||
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| // feat[BamUtils.CINDEX] = BamUtils.feat_class_index; | ||
| // feat[BamUtils.START] = br.pos; | ||
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| // // lref calc'd in dalliance/js/bam.js BamFile.readBamRecords() function | ||
| // if (br.lref) { // determine length based on CIGAR (lref is calc'd based on CIGAR string) | ||
| // feat[BamUtils.END] = br.pos + br.lref; | ||
| // } | ||
| // else { // determin length based on read length (no CIGAR found to calc lref) | ||
| // feat[BamUtils.END] = br.pos + br.seq.length; | ||
| // } | ||
| // //feat[END] = br.pos + br.lref; | ||
| // // feat.segment = br.segment; | ||
| // // feat.type = 'bam'; | ||
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| // // trying to determine orientation from 'XS' optional field | ||
| // if (br.XS === '-') { feat[BamUtils.STRAND] = -1; } | ||
| // else { feat[BamUtils.STRAND] = 1; } | ||
| // // var reverse = ((br.flag & 0x10) != 0); | ||
| // // feat[BamUtils.STRAND] = reverse ? -1 : 1; | ||
| // // feat[BamUtils.STRAND] = 1; // just calling starnd as forward for now | ||
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| // // simple ID, just same as readName | ||
| // // feat[BamUtils.ID] = br.readName; | ||
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| // // or possibly uniquify name by combining name, start, end (since read pairs etc. can have same readName): | ||
| // feat[BamUtils.ID] = br.readName + "/" + feat[BamUtils.START] + "-" + feat[BamUtils.END]; | ||
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| // // or to really guarantee uniqueness, combine name, start, end, cigar string | ||
| // // since different alignments of same read could have identical start and end, but | ||
| // // differing alignment in between (and therefore different CIGAR string) | ||
| // // feat[BamUtils.ID] = br.readName + "/" + feat[BamUtils.START] + "-" + feat[BamUtils.END] + "/" + feat[BamUtils.CIGAR]; | ||
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| // // feat.notes = ['Sequence=' + br.seq, 'CIGAR=' + br.cigar, 'MQ=' + br.mq]; | ||
| // // feat.seq = br.seq; // not having seq field in feat for now | ||
| // feat[BamUtils.CIGAR] = br.cigar; // cigar already translated from int array | ||
| // if (make_cigar_subfeats) { | ||
| // BamUtils.createSubfeats(feat); | ||
| // } | ||
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| get: function(name) { | ||
| return this.data[ name ]; | ||
| }, | ||
| tags: function() { | ||
| return this.store.featureKeys(); | ||
| } | ||
| }); | ||
| }); |