samscope-announce Mailing List for samscope
A lightweight OpenGL SAM/BAM viewer
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From: Kris P. <kr...@dn...> - 2012-04-06 09:09:45
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After getting some user feedback from the SEQanswers community I've
released a couple new versions, bringing us up to version 1.6.6.4. Since
the last announcement at 1.6.6, here's what's new!
* Fixes an SCons configuration error for some versions of SCons.
* Includes latest version of bamtools in internal distribution (2.1.1)
* Provides more detailed error messagse for broken SAM/BAM files.
* Fixes quality value bounding.
* Internal namespace cleaning.
* Fixes an SCons configuration error for some versions of SCons.
If you encounter broken BAM files ("no header data found") please send
me at least a failing excerpt, because I have yet to encounter one of
these files. Samscope uses bamtools for parsing BAM files, and
technically the SAM file spec demands that BAM files carry at least
*some* header data, so this seems to be a bamtools bug, but I can't
reproduce it with any of my BAM files to even attempt to diagnose it.
--
--Kris Popendorf
叶ってしまう夢は本当の夢と言えん。
[A dream that comes true can't really be called a dream.]
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From: Kris P. <kr...@dn...> - 2012-04-03 15:11:26
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I just pushed a new version, Samscope 1.6.6 onto all of the various servers. This version fixes a annoyances and adds a whole host of wishlist features. It's a highly recommended update for everyone! Major changes include: * Adds a line graph display of read quality. * Adds a visual line to show cursor position in read info. * Improves paste reliability for single and complex coordinates. * Fixes pasting from self (and bookmarks). * Adds direction specific mutation/call counting. * Adds option for drawing read detail from lower zooms. * Adds option for laying out pair ends as single end reads. * Adds detail coloring by base. * Improves visualization of links from vertically squished zooms. * Adds custom link types. * Adds a minimap for "situational awareness". -- --Kris Popendorf 叶ってしまう夢は本当の夢と言えん。 [A dream that comes true can't really be called a dream.] |
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From: Kris P. <kr...@dn...> - 2012-03-26 09:24:08
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After an unfortunate incident with an avocado and a kitchen knife, I was stuck in the hospital for about a month, but I'm back to work with at least 9 out of 10 fingers! (Hopefully back to all 10 soon!) I've just pushed version 1.6.5.2 to the servers. This version: * fixes some paired-end coloring errors * adds some missing documentation * adds a display of quality scores for each read I've got a few more things I'd like to add soon, so keep watching, and send any requests you might have! -- --Kris Popendorf 叶ってしまう夢は本当の夢と言えん。 [A dream that comes true can't really be called a dream.] |
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From: Kris P. <kr...@dn...> - 2012-02-19 16:13:04
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This release follows quickly on the heels of 1.6.4, adding the recently promised X11 selection support (rather than deprecated cut buffers). The full changelog entry is as follows: samscope (1.6.5) Mon, 20 Feb 2012 01:04:19 +0900 * Adds X11 selection support (*real* copy/paste) * Fixes build system when Xmu is unavailable. * Fixes seek behavior for inexact location specs. * Adds proper/improper/unpaired layers As always, let me know if you find a problem! -- --Kris Popendorf 叶ってしまう夢は本当の夢と言えん。 [A dream that comes true can't really be called a dream.] |
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From: Kris P. <kr...@dn...> - 2012-02-16 18:13:52
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I just pushed samscope 1.6.4 to all of the various servers. This version fixes some important (if embarassing) bugs, and adds some fairly awesome new features: * Fixes erroneous culling of consensus calls around origin * Fixes crash on rendering unmapped reads * Adds better coloring for link types (including improper pairs) * Adds alternate read coloring based purely on link types. * Adds "bookmarks" (copy/paste current location (C-b, C-v)) * Allows copying current inspection data to clipboard (C-c) Improper pairs can also be counted and built as layers using the --buildimproper option. Also note the new read coloring toggle for mutation vs pair-type (toggle with the 'm' key). The clipboard functionality is somewhat a work in progress and currently only uses X cut buffers (usually your mouse middle click button). X "selection" support will be added soon. Also, clipboard functionality adds a new dependency to the list (libxmu-dev) for those building from source. However libxmu, libdevil, and zlib will now automatically be disabled when not available, lessening the burden on those who don't care about the related features (clipboard, sceenshots, and compressed source files respectively). Enjoy! -- --Kris Popendorf 叶ってしまう夢は本当の夢と言えん。 [A dream that comes true can't really be called a dream.] |
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From: Kris P. <kr...@dn...> - 2012-02-15 14:00:09
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I just released version Samscope 1.6.3, and it's making it way through the compile build farms and will be hitting the servers soon. Version 1.6.3 adds the ability to produce exact consensus calls on bases when you mouse over them. Until now the mutation/base call data was an estimate drawn from the reads that had been actually drawn on screen thus far (which, if you had more reads than pixels might have been an incomplete sample). Now mousing over a base start exhaustively sampling all reads on that base, updating its mutation/call data and displaying whether or not it's an estimate or complete. This also updates other bases that are covered by the same read as well and is kind of neat to watch interactively. Please give it a try! --Kris Popendorf 叶ってしまう夢は本当の夢と言えん。 [A dream that comes true can't really be called a dream.] |
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From: Kris P. <kr...@dn...> - 2012-02-14 05:56:43
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As the number of users of Samscope picks up, I'll be using this mailing list to announce new releases. Samscope 1.6.2 has just been pushed onto all of the various servers. Notable changes from version 1.5.0 include: * Adds detailed display of reads when at mip0. * Fixes incorrect inference of reference sequence for some MD tags. * Added a "pan" tool for trackpad users. * Improved interface. * Makes dependency on ILUT optional. The display of detailed reads is actually very fast and very handy, so I highly recommend you try it! Send mail to sam...@li... if you have questions. -- --Kris Popendorf 叶ってしまう夢は本当の夢と言えん。 [A dream that comes true can't really be called a dream.] |
