Feature request: group BED tracks by strand #962
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@tfenne we already have this feature but its named poorly. In the popup menu is a "Set color (negative values)" option. For wig tracks this does just what it says, but for feature (bed, gff, etc) it sets the color of negative strand features. |
jrobinso
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I'm going to rename this to "Group", since that is something we don't have. Task is to implement a "group by ..." concept for feature tracks, similar to alignment tracks. |
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Ah, thanks @jrobinso - somehow I missed that! That's perfect. |
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jrobinso
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brainstorm
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brainstorm
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* Remove deprecated GA4GH classes. * Remove unused "lite" classes * Combine classes PicardAlignment -> SAMAlignment * Fix autoscale & group autoscale repaint problems * mm tag support * Introduce "ByteSubarray" to avoid copying read sequence and quality arrays * Add unit test * rename "isSoftClipped" -> "isSoftClip" for clarity * Add option to "color by base modification". See issue igvteam#945. TODO * parse and use likelihood scores. * resolve multiple modifications on a single base * add color scheme by modification type * add modificaton info to popup text * alpha-shade base modifications by likelihood * Draw base modification after base mismatches * base modifications -- parse all cases from spec * Change preference hierarchy behavior -- user settings for generic alignment tracks ("Alignments" tab) will now cascade down to RNA and 3rd gen alignments if there is no specific user setting for those types. * remove unused export * Add popup text for base modifications * Popup text for base modifications * update test * Bug fix -- file name used for track name in "load from server". Fixes igvteam#959 * Base modifications -- add stable colors for known modification types * Optionally write relative genome paths in sessions * Handle case of SAM record without base qualities * Add "Flags" to alignment record popup text. See issue igvteam#864 * Support base modifications in coverage track. See igvteam#945 * Group feature tracks by strand. Fixes igvteam#962
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It would be helpful on occasion (e.g. when reviewing tracks of primers/probes/etc.) to be able to color tracks derived from BED (and IntervalList) files by strands. Similarly would be useful to sort/group by strand too, but coloring by itself would be great.
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