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Trackster: better drawing of deletions in variant tracks. Initial parsing of insertions.

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This commit is contained in:
Jeremy Goecks
2014-10-24 15:04:06 -04:00
parent ba8c3bef28
commit d1eabea652
3 changed files with 73 additions and 77 deletions
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client/galaxy/scripts/viz/trackster/painters.js
+36 -38
View File
@@ -1402,32 +1402,38 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
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.
var
/**
* Returns dictionary of information about an indel; returns empty if there no indel. Assumes indel is left-aligned.
* Dict attributes:
* -type: 'insertion' or 'deletion'
* -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 );
};
get_indel_info = function(ref, alt) {
var ref_len = ref.length,
alt_len = alt.length,
start = 0,
len = 1,
type = null;
if (alt === '-') {
type = 'deletion';
len = ref.length;
}
else if (ref.indexOf(alt) === 0 && ref_len > alt_len) {
type = 'deletion';
len = ref_len - alt_len;
start = alt_len;
}
else if (alt.indexOf(ref) === 0 && ref_len < alt_len) {
// Insertion.
type = 'insertion';
len = alt_len - ref_len;
start = alt_len;
}
return ( type !== null ? { type: type, start: start, len: len } : {} );
};
// Draw.
var locus_data,
@@ -1488,22 +1494,14 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
// 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,
});
var alt_info = {
type: 'snp',
value: a,
start: 0
},
indel_info = get_indel_info(ref, a);
return _.extend(alt_info, indel_info);
});
// Only draw locus data if it's in viewing region.
@@ -1511,7 +1509,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
continue;
}
// Compute start for drawing variants marker, text.
// Compute start for drawing variants marker, text.
draw_x_start = Math.floor( Math.max(-0.5 * w_scale, (pos - this.view_start - 0.5) * w_scale) );
char_x_start = Math.floor( Math.max(0, (pos - this.view_start) * w_scale) );
static/scripts/packed/viz/trackster/painters.js
+1 -1
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static/scripts/viz/trackster/painters.js
+36 -38
View File
@@ -1402,32 +1402,38 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
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.
var
/**
* Returns dictionary of information about an indel; returns empty if there no indel. Assumes indel is left-aligned.
* Dict attributes:
* -type: 'insertion' or 'deletion'
* -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 );
};
get_indel_info = function(ref, alt) {
var ref_len = ref.length,
alt_len = alt.length,
start = 0,
len = 1,
type = null;
if (alt === '-') {
type = 'deletion';
len = ref.length;
}
else if (ref.indexOf(alt) === 0 && ref_len > alt_len) {
type = 'deletion';
len = ref_len - alt_len;
start = alt_len;
}
else if (alt.indexOf(ref) === 0 && ref_len < alt_len) {
// Insertion.
type = 'insertion';
len = alt_len - ref_len;
start = alt_len;
}
return ( type !== null ? { type: type, start: start, len: len } : {} );
};
// Draw.
var locus_data,
@@ -1488,22 +1494,14 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
// 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,
});
var alt_info = {
type: 'snp',
value: a,
start: 0
},
indel_info = get_indel_info(ref, a);
return _.extend(alt_info, indel_info);
});
// Only draw locus data if it's in viewing region.
@@ -1511,7 +1509,7 @@ _.extend(VariantPainter.prototype, Painter.prototype, {
continue;
}
// Compute start for drawing variants marker, text.
// Compute start for drawing variants marker, text.
draw_x_start = Math.floor( Math.max(-0.5 * w_scale, (pos - this.view_start - 0.5) * w_scale) );
char_x_start = Math.floor( Math.max(0, (pos - this.view_start) * w_scale) );