1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/c0eb0f44b7fe/ Changeset: c0eb0f44b7fe User: jgoecks Date: 2013-11-18 19:55:43 Summary: Trackster: add support for detecting and drawing deletions in VCF datasets. Create shared read painter utils that are used by multiple painters. Affected #: 1 file

diff -r a0120448a28eeda50a0476a6d46da74ad3afa484 -r c0eb0f44b7fe80fdcb6590c4364312bbdcb286b0 static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -749,7 +749,8 @@ gap = Math.round(w_scale/2), char_width_px = ctx.canvas.manager.char_width_px, block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color), - pack_mode = (mode === 'Pack'); + pack_mode = (mode === 'Pack'), + paint_utils = new ReadPainterUtils(ctx, (pack_mode ? PACK_FEATURE_HEIGHT : SQUISH_FEATURE_HEIGHT), w_scale);

// Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; @@ -847,8 +848,7 @@ base_offset += cig_len; break; case "D": // Deletion. - ctx.fillStyle = "black"; - ctx.fillRect(s_start, y_center + 4, s_end - s_start, 3); + paint_utils.draw_deletion(s_start, y_center, 1); base_offset += cig_len; break; case "P": // TODO: No good way to draw insertions/padding right now, so ignore @@ -1507,6 +1507,27 @@ };

/** + * Utilities for painting reads. + */ +var ReadPainterUtils = function(ctx, row_height, char_width) { + this.ctx = ctx; + this.row_height = row_height; + this.char_width = char_width; +}; + +extend(ReadPainterUtils.prototype, { + /** + * Draw deletion of base(s). + */ + draw_deletion: function(x, y, len) { + this.ctx.fillStyle = "black"; + var thickness = Math.max( 0.25 * this.row_height, 1 ); + y += 0.5 * ( this.row_height - thickness ); + this.ctx.fillRect( x, y + 4, len * this.char_width, thickness); + } +}); + +/** * Paints variant data onto canvas. */ var VariantPainter = function(data, view_start, view_end, prefs, mode, base_color_fn) { @@ -1556,6 +1577,34 @@ draw: function(ctx, width, height, w_scale) { ctx.save();

+ // Functions for detection insertions (TODO) and deletions. + + /** Returns dictionary of information about a deletion; returns null if there no deletion. + * Dict attributes: + * -start: where the deletion starts relative to reference start + * -len: how long the deletion is + */ + var get_deletion_info = function(ref, alt) { + var ref_len = ref.length, + alt_len = alt.length, + start = 0, + len = 1, + is_delete = false; + if (alt === '-') { + is_delete = true; + len = ref.length; + } + else if (ref.indexOf(alt) === 0 && ref_len > alt_len) { + is_delete = true; + len = ref_len = alt_len; + start += alt_len; + } + + return ( is_delete ? { start: start, len: len } : null ); + }; + + + // Draw. var locus_data, pos, id, @@ -1582,6 +1631,7 @@ (this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT) ), draw_summary = true, + paint_utils = new ReadPainterUtils(ctx, row_height, base_px), j;

// If there's a single sample, update drawing variables. @@ -1605,10 +1655,31 @@ // Get locus data. locus_data = this.data[i]; pos = locus_data[1]; - alt = locus_data[4].split(','); + ref = locus_data[3]; + alt = [ locus_data[4].split(',') ]; sample_gts = locus_data[7].split(','); allele_counts = locus_data.slice(8);

+ // Process alterate values to derive information about each alt. + alt = _.map(_.flatten(alt), function(a) { + var type, + alt_info = {}, + delete_info = get_deletion_info(ref, a); + if (delete_info) { + type = 'deletion'; + _.extend(alt_info, delete_info); + } + // TODO: test for insertion. + else { // SNP. + type = 'snp'; + } + + return _.extend(alt_info, { + type: type, + value: a, + }); + }); + // Only draw locus data if it's in viewing region. if (pos < this.view_start || pos > this.view_end) { continue; @@ -1627,7 +1698,7 @@ draw_y_start = this.prefs.summary_height; // Draw allele fractions onto summary. for (j = 0; j < alt.length; j++) { - ctx.fillStyle = this.base_color_fn(alt[j]); + ctx.fillStyle = ( alt[j].type === 'deletion' ? 'black' : this.base_color_fn(alt[j].value) ); allele_frac = allele_counts / sample_gts.length; draw_height = Math.ceil(this.prefs.summary_height * allele_frac); ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height); @@ -1664,12 +1735,21 @@

// If there's a variant, draw it. if (variant) { - ctx.fillStyle = this.base_color_fn(variant); - if (this.mode === 'Squish' || w_scale < ctx.canvas.manager.char_width_px) { - ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); + if (variant.type === 'snp') { + var snp = variant.value; + ctx.fillStyle = this.base_color_fn(snp); + if (this.mode === 'Squish' || w_scale < ctx.canvas.manager.char_width_px) { + ctx.fillRect(draw_x_start, draw_y_start + 1, base_px, feature_height); + } + else { + ctx.fillText(snp, char_x_start, draw_y_start + row_height); + } + } + else if (variant.type === 'deletion') { + paint_utils.draw_deletion(draw_x_start + base_px * variant.start, draw_y_start, variant.len); } else { - ctx.fillText(variant, char_x_start, draw_y_start + row_height); + // TODO: handle insertions. } } }

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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