René's URL Explorer Experiment

Title: History for samplot/samplot_vcf.py - grosscol/samplot · GitHub

Open Graph Title: History for samplot/samplot_vcf.py - grosscol/samplot

X Title: History for samplot/samplot_vcf.py - grosscol/samplot

Description: Plot structural variant signals from many BAMs and CRAMs - History for samplot/samplot_vcf.py - grosscol/samplot

Open Graph Description: Plot structural variant signals from many BAMs and CRAMs - History for samplot/samplot_vcf.py - grosscol/samplot

X Description: Plot structural variant signals from many BAMs and CRAMs - History for samplot/samplot_vcf.py - grosscol/samplot

Opengraph URL: https://github.com/grosscol/samplot

X: @github

direct link

Domain: github.com

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Links:

Skip to content	https://github.com/grosscol/samplot/commits/master/samplot/samplot_vcf.py#start-of-content
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Reload	https://github.com/grosscol/samplot/commits/master/samplot/samplot_vcf.py
Reload	https://github.com/grosscol/samplot/commits/master/samplot/samplot_vcf.py
Reload	https://github.com/grosscol/samplot/commits/master/samplot/samplot_vcf.py
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samplot_vcf.py	https://github.com/grosscol/samplot/commits/master/samplot/samplot_vcf.py
master	https://github.com/grosscol/samplot/tree/master
Merge pull request #193 from pontushojer/warn-missing-samples	https://github.com/grosscol/samplot/commit/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59
	https://github.com/ryanlayer
ryanlayer	https://github.com/grosscol/samplot/commits?author=ryanlayer
dfc8609	https://github.com/grosscol/samplot/commit/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59
	https://github.com/grosscol/samplot/blob/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59
warn if missing samples in BAMs or VCF	https://github.com/grosscol/samplot/commit/b0e450ac55c1be249c11baecfec1af7a4437d326
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
b0e450a	https://github.com/grosscol/samplot/commit/b0e450ac55c1be249c11baecfec1af7a4437d326
	https://github.com/grosscol/samplot/blob/b0e450ac55c1be249c11baecfec1af7a4437d326/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/b0e450ac55c1be249c11baecfec1af7a4437d326
enable dysgu translocations	https://github.com/grosscol/samplot/commit/ef7a2941e148081ea936f64c9af08543404f3977
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
ef7a294	https://github.com/grosscol/samplot/commit/ef7a2941e148081ea936f64c9af08543404f3977
	https://github.com/grosscol/samplot/blob/ef7a2941e148081ea936f64c9af08543404f3977/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/ef7a2941e148081ea936f64c9af08543404f3977
fix bug where 2nd breakpoint position not in INFO/END for interchromosomal translocations	https://github.com/grosscol/samplot/commit/55a85fbaef996a72d508a3ac18190462f54ef417
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
55a85fb	https://github.com/grosscol/samplot/commit/55a85fbaef996a72d508a3ac18190462f54ef417
	https://github.com/grosscol/samplot/blob/55a85fbaef996a72d508a3ac18190462f54ef417/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/55a85fbaef996a72d508a3ac18190462f54ef417
fix missing space in template for translocations	https://github.com/grosscol/samplot/commit/b3a2f7ae79a90513996584a5d4906afe6d9aea34
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
b3a2f7a	https://github.com/grosscol/samplot/commit/b3a2f7ae79a90513996584a5d4906afe6d9aea34
	https://github.com/grosscol/samplot/blob/b3a2f7ae79a90513996584a5d4906afe6d9aea34/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/b3a2f7ae79a90513996584a5d4906afe6d9aea34
Add parenthesis	https://github.com/grosscol/samplot/commit/26337772ce4b3890b3a3fc9d62260d4fc241d691
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
2633777	https://github.com/grosscol/samplot/commit/26337772ce4b3890b3a3fc9d62260d4fc241d691
	https://github.com/grosscol/samplot/blob/26337772ce4b3890b3a3fc9d62260d4fc241d691/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/26337772ce4b3890b3a3fc9d62260d4fc241d691
fix translocation handling and add log messages	https://github.com/grosscol/samplot/commit/ccefb81ab864f9817ac2cc431a73b3988554a777
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
ccefb81	https://github.com/grosscol/samplot/commit/ccefb81ab864f9817ac2cc431a73b3988554a777
	https://github.com/grosscol/samplot/blob/ccefb81ab864f9817ac2cc431a73b3988554a777/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/ccefb81ab864f9817ac2cc431a73b3988554a777
add info about how many variants are filtered out.	https://github.com/grosscol/samplot/commit/ceb48c62571accef0ef0bec77b0002e55d4de7f9
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
ceb48c6	https://github.com/grosscol/samplot/commit/ceb48c62571accef0ef0bec77b0002e55d4de7f9
	https://github.com/grosscol/samplot/blob/ceb48c62571accef0ef0bec77b0002e55d4de7f9/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/ceb48c62571accef0ef0bec77b0002e55d4de7f9
fix string formatting	https://github.com/grosscol/samplot/commit/80b4f2f2728df3109d47952d7964f11b2a31226a
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
80b4f2f	https://github.com/grosscol/samplot/commit/80b4f2f2728df3109d47952d7964f11b2a31226a
	https://github.com/grosscol/samplot/blob/80b4f2f2728df3109d47952d7964f11b2a31226a/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/80b4f2f2728df3109d47952d7964f11b2a31226a
Exit if no samples in VCF match sample in BAMs or those specified using `--sample_ids`.	https://github.com/grosscol/samplot/commit/12aad6f1143cea338191baacf9a51253f7747d96
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
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	https://github.com/grosscol/samplot/blob/12aad6f1143cea338191baacf9a51253f7747d96/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/12aad6f1143cea338191baacf9a51253f7747d96
use logger for messages	https://github.com/grosscol/samplot/commit/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
4a5505f	https://github.com/grosscol/samplot/commit/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
	https://github.com/grosscol/samplot/blob/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
Merge pull request #150 from pontushojer/vcf-multithread	https://github.com/grosscol/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
	https://github.com/mchowdh200
mchowdh200	https://github.com/grosscol/samplot/commits?author=mchowdh200
4ac4ce0	https://github.com/grosscol/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
	https://github.com/grosscol/samplot/blob/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
Enable multithread plotting from VCF	https://github.com/grosscol/samplot/commit/152031a81cf4d572721c9cdf4515acb569ea8b4f
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
152031a	https://github.com/grosscol/samplot/commit/152031a81cf4d572721c9cdf4515acb569ea8b4f
	https://github.com/grosscol/samplot/blob/152031a81cf4d572721c9cdf4515acb569ea8b4f/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/152031a81cf4d572721c9cdf4515acb569ea8b4f
Enable plot generation without using subprocess	https://github.com/grosscol/samplot/commit/b96a1f9304a2887f93a73baf82b163864b097c7f
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
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	https://github.com/grosscol/samplot/blob/b96a1f9304a2887f93a73baf82b163864b097c7f/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/b96a1f9304a2887f93a73baf82b163864b097c7f
Remove unused functions identified with (vulture)[https://github.com/jendrikseipp/vulture]	https://github.com/grosscol/samplot/commit/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
	https://github.com/pontushojer
pontushojer	https://github.com/grosscol/samplot/commits?author=pontushojer
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	https://github.com/grosscol/samplot/blob/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
Allow manual scaling of annotation track size and other fixes (#141)	https://github.com/grosscol/samplot/commit/a1c1342930ae433e6f9672b3226a2bc22283389b
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
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	https://github.com/grosscol/samplot/blob/a1c1342930ae433e6f9672b3226a2bc22283389b/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/a1c1342930ae433e6f9672b3226a2bc22283389b
removed unset FORMAT fields and changed gff to gff3 explicitly	https://github.com/grosscol/samplot/commit/eadc0934a3450b67ac2faa75be9e716c4b5e8174
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
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	https://github.com/grosscol/samplot/blob/eadc0934a3450b67ac2faa75be9e716c4b5e8174/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/eadc0934a3450b67ac2faa75be9e716c4b5e8174
removes get_overlap bug	https://github.com/grosscol/samplot/commit/3ecad660da84a0bf5f8ea6c464f016ba66be0a84
3ecad66	https://github.com/grosscol/samplot/commit/3ecad660da84a0bf5f8ea6c464f016ba66be0a84
	https://github.com/grosscol/samplot/blob/3ecad660da84a0bf5f8ea6c464f016ba66be0a84/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/3ecad660da84a0bf5f8ea6c464f016ba66be0a84
fixed bug in control-sample truncation	https://github.com/grosscol/samplot/commit/81e9b6028f1eb6a60df63f9168e1baee24a9be7d
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
81e9b60	https://github.com/grosscol/samplot/commit/81e9b6028f1eb6a60df63f9168e1baee24a9be7d
	https://github.com/grosscol/samplot/blob/81e9b6028f1eb6a60df63f9168e1baee24a9be7d/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/81e9b6028f1eb6a60df63f9168e1baee24a9be7d
bugfixes for errors in vcf with translocations and CIs	https://github.com/grosscol/samplot/commit/3501f147a7dc62f7a4ec629abaaa8a7f8fb79872
	https://github.com/jbelyeu
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	https://github.com/grosscol/samplot/blob/3501f147a7dc62f7a4ec629abaaa8a7f8fb79872/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/3501f147a7dc62f7a4ec629abaaa8a7f8fb79872
fixed bug in translocation case samplot vcf	https://github.com/grosscol/samplot/commit/650736b1216de3bbf54151e166303b8bbab23c37
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
650736b	https://github.com/grosscol/samplot/commit/650736b1216de3bbf54151e166303b8bbab23c37
	https://github.com/grosscol/samplot/blob/650736b1216de3bbf54151e166303b8bbab23c37/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/650736b1216de3bbf54151e166303b8bbab23c37
added support for bnds in samplot vcf	https://github.com/grosscol/samplot/commit/ebf1300e03fff68c0569dd1992f1940ac1810712
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
ebf1300	https://github.com/grosscol/samplot/commit/ebf1300e03fff68c0569dd1992f1940ac1810712
	https://github.com/grosscol/samplot/blob/ebf1300e03fff68c0569dd1992f1940ac1810712/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/ebf1300e03fff68c0569dd1992f1940ac1810712
added debug option	https://github.com/grosscol/samplot/commit/b16eafcb5e12f235c125dd736ae519f222828fdf
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
b16eafc	https://github.com/grosscol/samplot/commit/b16eafcb5e12f235c125dd736ae519f222828fdf
	https://github.com/grosscol/samplot/blob/b16eafcb5e12f235c125dd736ae519f222828fdf/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/b16eafcb5e12f235c125dd736ae519f222828fdf
removed minq from samplot_vcf	https://github.com/grosscol/samplot/commit/40c9c1bc5d61246a8b17f433a6bbbcc3b04da53d
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
40c9c1b	https://github.com/grosscol/samplot/commit/40c9c1bc5d61246a8b17f433a6bbbcc3b04da53d
	https://github.com/grosscol/samplot/blob/40c9c1bc5d61246a8b17f433a6bbbcc3b04da53d/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/40c9c1bc5d61246a8b17f433a6bbbcc3b04da53d
linted and removed unused vars	https://github.com/grosscol/samplot/commit/2c21bd617d81e7c640fade424622336c5b0205ff
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
2c21bd6	https://github.com/grosscol/samplot/commit/2c21bd617d81e7c640fade424622336c5b0205ff
	https://github.com/grosscol/samplot/blob/2c21bd617d81e7c640fade424622336c5b0205ff/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/2c21bd617d81e7c640fade424622336c5b0205ff
added min window size	https://github.com/grosscol/samplot/commit/6057299b23acd467b4049430ce0caafff8db50b5
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
6057299	https://github.com/grosscol/samplot/commit/6057299b23acd467b4049430ce0caafff8db50b5
	https://github.com/grosscol/samplot/blob/6057299b23acd467b4049430ce0caafff8db50b5/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/6057299b23acd467b4049430ce0caafff8db50b5
fixed params issue, template install problem	https://github.com/grosscol/samplot/commit/b58c91c25f755d65134e74603ce337e37ccec885
	https://github.com/jbelyeu
jbelyeu	https://github.com/grosscol/samplot/commits?author=jbelyeu
b58c91c	https://github.com/grosscol/samplot/commit/b58c91c25f755d65134e74603ce337e37ccec885
	https://github.com/grosscol/samplot/blob/b58c91c25f755d65134e74603ce337e37ccec885/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/b58c91c25f755d65134e74603ce337e37ccec885
Updates `samplot vcf` (#19)	https://github.com/grosscol/samplot/commit/0aa03b6a830892ce34aa0bcd399b1ed9f1d6066b
0aa03b6	https://github.com/grosscol/samplot/commit/0aa03b6a830892ce34aa0bcd399b1ed9f1d6066b
	https://github.com/grosscol/samplot/blob/0aa03b6a830892ce34aa0bcd399b1ed9f1d6066b/samplot/samplot_vcf.py
	https://github.com/grosscol/samplot/tree/0aa03b6a830892ce34aa0bcd399b1ed9f1d6066b
	https://github.com
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