SAM flag info on hover/click #864
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I've added this in a branch dedicated to other alignment track improvements, but it won't be released right away. It turns out it would be disruptive for a point release due to the class hierarchy in the current 2.9.X branch. I anticipate releasing 2.10, which has this addition, in early June. |
jrobinso
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May 21, 2021
* 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 #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 #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 #864 * Support base modifications in coverage track. See #945 * Group feature tracks by strand. Fixes #962
brainstorm
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Jun 11, 2021
* 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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Hi,
Thanks for keep developing IGV. To be honest everyday i realise another useful trick of it.
I would like to add SAM Flag to the hover/click window like I shared below. Is this possible? because i couldnt find it through preference > alignment.
I also checked here but I wasnt lucky enough. --> https://groups.google.com/g/igv-help/search?q=sam%20flag
My IGV version is 2.4.19
Thank you very much for your help,
Best,
T.
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