René's URL Explorer Experiment


Title: History for samplot - Knnnk/samplot · GitHub

Open Graph Title: History for samplot - Knnnk/samplot

X Title: History for samplot - Knnnk/samplot

Description: Plot structural variant signals from many BAMs and CRAMs - History for samplot - Knnnk/samplot

Open Graph Description: Plot structural variant signals from many BAMs and CRAMs - History for samplot - Knnnk/samplot

X Description: Plot structural variant signals from many BAMs and CRAMs - History for samplot - Knnnk/samplot

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

X: @github

direct link

Domain: github.com

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samplothttps://github.com/Knnnk/samplot/commits/master/samplot
masterhttps://github.com/Knnnk/samplot/tree/master
Update samplot/samplot.pyhttps://github.com/Knnnk/samplot/commit/8e5f9c9e9278bcf428df361beb5c5e7fd3c3d18f
kdm9https://github.com/Knnnk/samplot/commits?author=kdm9
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
8e5f9c9https://github.com/Knnnk/samplot/commit/8e5f9c9e9278bcf428df361beb5c5e7fd3c3d18f
https://github.com/Knnnk/samplot/blob/8e5f9c9e9278bcf428df361beb5c5e7fd3c3d18f/samplot
https://github.com/Knnnk/samplot/tree/8e5f9c9e9278bcf428df361beb5c5e7fd3c3d18f
fixes for python 3.11https://github.com/Knnnk/samplot/commit/444f3bdde8d74e86173ce6dee824fccfae409371
https://github.com/kdm9
kdm9https://github.com/Knnnk/samplot/commits?author=kdm9
444f3bdhttps://github.com/Knnnk/samplot/commit/444f3bdde8d74e86173ce6dee824fccfae409371
https://github.com/Knnnk/samplot/blob/444f3bdde8d74e86173ce6dee824fccfae409371/samplot
https://github.com/Knnnk/samplot/tree/444f3bdde8d74e86173ce6dee824fccfae409371
Merge pull request #193 from pontushojer/warn-missing-sampleshttps://github.com/Knnnk/samplot/commit/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
dfc8609https://github.com/Knnnk/samplot/commit/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59
https://github.com/Knnnk/samplot/blob/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59/samplot
https://github.com/Knnnk/samplot/tree/dfc8609dbdd028b67f6e8ff2bb3437c5161c6b59
warn if missing samples in BAMs or VCFhttps://github.com/Knnnk/samplot/commit/b0e450ac55c1be249c11baecfec1af7a4437d326
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
b0e450ahttps://github.com/Knnnk/samplot/commit/b0e450ac55c1be249c11baecfec1af7a4437d326
https://github.com/Knnnk/samplot/blob/b0e450ac55c1be249c11baecfec1af7a4437d326/samplot
https://github.com/Knnnk/samplot/tree/b0e450ac55c1be249c11baecfec1af7a4437d326
enable dysgu translocationshttps://github.com/Knnnk/samplot/commit/ef7a2941e148081ea936f64c9af08543404f3977
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
ef7a294https://github.com/Knnnk/samplot/commit/ef7a2941e148081ea936f64c9af08543404f3977
https://github.com/Knnnk/samplot/blob/ef7a2941e148081ea936f64c9af08543404f3977/samplot
https://github.com/Knnnk/samplot/tree/ef7a2941e148081ea936f64c9af08543404f3977
fix bug where 2nd breakpoint position not in INFO/END for interchromosomal translocationshttps://github.com/Knnnk/samplot/commit/55a85fbaef996a72d508a3ac18190462f54ef417
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
55a85fbhttps://github.com/Knnnk/samplot/commit/55a85fbaef996a72d508a3ac18190462f54ef417
https://github.com/Knnnk/samplot/blob/55a85fbaef996a72d508a3ac18190462f54ef417/samplot
https://github.com/Knnnk/samplot/tree/55a85fbaef996a72d508a3ac18190462f54ef417
fix missing space in template for translocationshttps://github.com/Knnnk/samplot/commit/b3a2f7ae79a90513996584a5d4906afe6d9aea34
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
b3a2f7ahttps://github.com/Knnnk/samplot/commit/b3a2f7ae79a90513996584a5d4906afe6d9aea34
https://github.com/Knnnk/samplot/blob/b3a2f7ae79a90513996584a5d4906afe6d9aea34/samplot
https://github.com/Knnnk/samplot/tree/b3a2f7ae79a90513996584a5d4906afe6d9aea34
Add parenthesishttps://github.com/Knnnk/samplot/commit/26337772ce4b3890b3a3fc9d62260d4fc241d691
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
2633777https://github.com/Knnnk/samplot/commit/26337772ce4b3890b3a3fc9d62260d4fc241d691
https://github.com/Knnnk/samplot/blob/26337772ce4b3890b3a3fc9d62260d4fc241d691/samplot
https://github.com/Knnnk/samplot/tree/26337772ce4b3890b3a3fc9d62260d4fc241d691
fix translocation handling and add log messageshttps://github.com/Knnnk/samplot/commit/ccefb81ab864f9817ac2cc431a73b3988554a777
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
ccefb81https://github.com/Knnnk/samplot/commit/ccefb81ab864f9817ac2cc431a73b3988554a777
https://github.com/Knnnk/samplot/blob/ccefb81ab864f9817ac2cc431a73b3988554a777/samplot
https://github.com/Knnnk/samplot/tree/ccefb81ab864f9817ac2cc431a73b3988554a777
Remove `np.int` depreciated in numpy 1.24.0https://github.com/Knnnk/samplot/commit/44d8685e91885e93f29a96a6e023e232667d03cc
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
44d8685https://github.com/Knnnk/samplot/commit/44d8685e91885e93f29a96a6e023e232667d03cc
https://github.com/Knnnk/samplot/blob/44d8685e91885e93f29a96a6e023e232667d03cc/samplot
https://github.com/Knnnk/samplot/tree/44d8685e91885e93f29a96a6e023e232667d03cc
Merge pull request #183 from pontushojer/jitter-longhttps://github.com/Knnnk/samplot/commit/db2ba62a68b51cd44faeb18f307561e3f14fbb89
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
db2ba62https://github.com/Knnnk/samplot/commit/db2ba62a68b51cd44faeb18f307561e3f14fbb89
https://github.com/Knnnk/samplot/blob/db2ba62a68b51cd44faeb18f307561e3f14fbb89/samplot
https://github.com/Knnnk/samplot/tree/db2ba62a68b51cd44faeb18f307561e3f14fbb89
Merge pull request #179 from pontushojer/coverage-speeduphttps://github.com/Knnnk/samplot/commit/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
dbf629fhttps://github.com/Knnnk/samplot/commit/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce
https://github.com/Knnnk/samplot/blob/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce/samplot
https://github.com/Knnnk/samplot/tree/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce
Merge pull request #178 from pontushojer/variants-statshttps://github.com/Knnnk/samplot/commit/011c793c74799df98c71d584602e5100f7f25af8
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
011c793https://github.com/Knnnk/samplot/commit/011c793c74799df98c71d584602e5100f7f25af8
https://github.com/Knnnk/samplot/blob/011c793c74799df98c71d584602e5100f7f25af8/samplot
https://github.com/Knnnk/samplot/tree/011c793c74799df98c71d584602e5100f7f25af8
Use same offset at both ends of bent line and make the line bends up for large jitter_bounds.https://github.com/Knnnk/samplot/commit/202b1038e1db985b6ba35554f78e60308ea0278e
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
202b103https://github.com/Knnnk/samplot/commit/202b1038e1db985b6ba35554f78e60308ea0278e
https://github.com/Knnnk/samplot/blob/202b1038e1db985b6ba35554f78e60308ea0278e/samplot
https://github.com/Knnnk/samplot/tree/202b1038e1db985b6ba35554f78e60308ea0278e
simplify curr_max_insert_size updatehttps://github.com/Knnnk/samplot/commit/575dc9fcdcdb859c7ec52147fc3aa0fc7aff2d03
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
575dc9fhttps://github.com/Knnnk/samplot/commit/575dc9fcdcdb859c7ec52147fc3aa0fc7aff2d03
https://github.com/Knnnk/samplot/blob/575dc9fcdcdb859c7ec52147fc3aa0fc7aff2d03/samplot
https://github.com/Knnnk/samplot/tree/575dc9fcdcdb859c7ec52147fc3aa0fc7aff2d03
Enable --jitter for long readshttps://github.com/Knnnk/samplot/commit/ee99ec0c50e2a1c48ee523bd821a3d7a9ad49b16
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
ee99ec0https://github.com/Knnnk/samplot/commit/ee99ec0c50e2a1c48ee523bd821a3d7a9ad49b16
https://github.com/Knnnk/samplot/blob/ee99ec0c50e2a1c48ee523bd821a3d7a9ad49b16/samplot
https://github.com/Knnnk/samplot/tree/ee99ec0c50e2a1c48ee523bd821a3d7a9ad49b16
fix Missing legend (?) #171. Only include legends for read types that appear in the plot.https://github.com/Knnnk/samplot/commit/0bed14cf7aa8ee30859058a88d1bfa78d187caa3
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
0bed14chttps://github.com/Knnnk/samplot/commit/0bed14cf7aa8ee30859058a88d1bfa78d187caa3
https://github.com/Knnnk/samplot/blob/0bed14cf7aa8ee30859058a88d1bfa78d187caa3/samplot
https://github.com/Knnnk/samplot/tree/0bed14cf7aa8ee30859058a88d1bfa78d187caa3
speed up read coverage collectionhttps://github.com/Knnnk/samplot/commit/a5a4933a358b895d593246f928ddd1f0660c7a30
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
a5a4933https://github.com/Knnnk/samplot/commit/a5a4933a358b895d593246f928ddd1f0660c7a30
https://github.com/Knnnk/samplot/blob/a5a4933a358b895d593246f928ddd1f0660c7a30/samplot
https://github.com/Knnnk/samplot/tree/a5a4933a358b895d593246f928ddd1f0660c7a30
add info about how many variants are filtered out.https://github.com/Knnnk/samplot/commit/ceb48c62571accef0ef0bec77b0002e55d4de7f9
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
ceb48c6https://github.com/Knnnk/samplot/commit/ceb48c62571accef0ef0bec77b0002e55d4de7f9
https://github.com/Knnnk/samplot/blob/ceb48c62571accef0ef0bec77b0002e55d4de7f9/samplot
https://github.com/Knnnk/samplot/tree/ceb48c62571accef0ef0bec77b0002e55d4de7f9
fix string formattinghttps://github.com/Knnnk/samplot/commit/80b4f2f2728df3109d47952d7964f11b2a31226a
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
80b4f2fhttps://github.com/Knnnk/samplot/commit/80b4f2f2728df3109d47952d7964f11b2a31226a
https://github.com/Knnnk/samplot/blob/80b4f2f2728df3109d47952d7964f11b2a31226a/samplot
https://github.com/Knnnk/samplot/tree/80b4f2f2728df3109d47952d7964f11b2a31226a
Exit if no samples in VCF match sample in BAMs or those specified using `--sample_ids`.https://github.com/Knnnk/samplot/commit/12aad6f1143cea338191baacf9a51253f7747d96
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
12aad6fhttps://github.com/Knnnk/samplot/commit/12aad6f1143cea338191baacf9a51253f7747d96
https://github.com/Knnnk/samplot/blob/12aad6f1143cea338191baacf9a51253f7747d96/samplot
https://github.com/Knnnk/samplot/tree/12aad6f1143cea338191baacf9a51253f7747d96
Merge branch 'master' of https://github.com/pontushojer/samplothttps://github.com/Knnnk/samplot/commit/f03050860a21c71e39d512d6e7068dbc87b8e117
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
f030508https://github.com/Knnnk/samplot/commit/f03050860a21c71e39d512d6e7068dbc87b8e117
https://github.com/Knnnk/samplot/blob/f03050860a21c71e39d512d6e7068dbc87b8e117/samplot
https://github.com/Knnnk/samplot/tree/f03050860a21c71e39d512d6e7068dbc87b8e117
use logger for messageshttps://github.com/Knnnk/samplot/commit/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
4a5505fhttps://github.com/Knnnk/samplot/commit/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
https://github.com/Knnnk/samplot/blob/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e/samplot
https://github.com/Knnnk/samplot/tree/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
Show a popup error when an image is missinghttps://github.com/Knnnk/samplot/commit/e2180f07c35b5356612bc3790e7d39d9f3135a41
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
e2180f0https://github.com/Knnnk/samplot/commit/e2180f07c35b5356612bc3790e7d39d9f3135a41
https://github.com/Knnnk/samplot/blob/e2180f07c35b5356612bc3790e7d39d9f3135a41/samplot
https://github.com/Knnnk/samplot/tree/e2180f07c35b5356612bc3790e7d39d9f3135a41
fix tests and chr prefix strip (#168)https://github.com/Knnnk/samplot/commit/16560c18bfaf102933c4a7b89e3b28b9230b41d5
https://github.com/jbelyeu
jbelyeuhttps://github.com/Knnnk/samplot/commits?author=jbelyeu
16560c1https://github.com/Knnnk/samplot/commit/16560c18bfaf102933c4a7b89e3b28b9230b41d5
https://github.com/Knnnk/samplot/blob/16560c18bfaf102933c4a7b89e3b28b9230b41d5/samplot
https://github.com/Knnnk/samplot/tree/16560c18bfaf102933c4a7b89e3b28b9230b41d5
Merge pull request #157 from pontushojer/names-missinghttps://github.com/Knnnk/samplot/commit/f3968cf7f0412afa156018e747d6d870d718503f
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
f3968cfhttps://github.com/Knnnk/samplot/commit/f3968cf7f0412afa156018e747d6d870d718503f
https://github.com/Knnnk/samplot/blob/f3968cf7f0412afa156018e747d6d870d718503f/samplot
https://github.com/Knnnk/samplot/tree/f3968cf7f0412afa156018e747d6d870d718503f
Handle case where a gene entry from a GFF is missing the "Name" attribute.https://github.com/Knnnk/samplot/commit/533c81b7cb368330f74a5c861082583d843cbbd3
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
533c81bhttps://github.com/Knnnk/samplot/commit/533c81b7cb368330f74a5c861082583d843cbbd3
https://github.com/Knnnk/samplot/blob/533c81b7cb368330f74a5c861082583d843cbbd3/samplot
https://github.com/Knnnk/samplot/tree/533c81b7cb368330f74a5c861082583d843cbbd3
Transcript and exons should end exactly on defined position. Default capstyle project these outside of start/end positionshttps://github.com/Knnnk/samplot/commit/69209cadd1779b0515edd12fb08b64d34cf87a79
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
69209cahttps://github.com/Knnnk/samplot/commit/69209cadd1779b0515edd12fb08b64d34cf87a79
https://github.com/Knnnk/samplot/blob/69209cadd1779b0515edd12fb08b64d34cf87a79/samplot
https://github.com/Knnnk/samplot/tree/69209cadd1779b0515edd12fb08b64d34cf87a79
Move transcript name to top of drawinghttps://github.com/Knnnk/samplot/commit/091a9e2f17ec69c2e3211caad1e31237aab616e5
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
091a9e2https://github.com/Knnnk/samplot/commit/091a9e2f17ec69c2e3211caad1e31237aab616e5
https://github.com/Knnnk/samplot/blob/091a9e2f17ec69c2e3211caad1e31237aab616e5/samplot
https://github.com/Knnnk/samplot/tree/091a9e2f17ec69c2e3211caad1e31237aab616e5
Move arrows into transcripts and add multiple throughout transcript at regular intervals.https://github.com/Knnnk/samplot/commit/d5cc9d60a433c9dec97b441d471d663bd118c0dc
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
d5cc9d6https://github.com/Knnnk/samplot/commit/d5cc9d60a433c9dec97b441d471d663bd118c0dc
https://github.com/Knnnk/samplot/blob/d5cc9d60a433c9dec97b441d471d663bd118c0dc/samplot
https://github.com/Knnnk/samplot/tree/d5cc9d60a433c9dec97b441d471d663bd118c0dc
Unstack overlapping transcriptshttps://github.com/Knnnk/samplot/commit/fdbdb26fa50d208bc127711a00e8e080a970b448
https://github.com/pontushojer
pontushojerhttps://github.com/Knnnk/samplot/commits?author=pontushojer
fdbdb26https://github.com/Knnnk/samplot/commit/fdbdb26fa50d208bc127711a00e8e080a970b448
https://github.com/Knnnk/samplot/blob/fdbdb26fa50d208bc127711a00e8e080a970b448/samplot
https://github.com/Knnnk/samplot/tree/fdbdb26fa50d208bc127711a00e8e080a970b448
typo in help string for jitterhttps://github.com/Knnnk/samplot/commit/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
92fa270https://github.com/Knnnk/samplot/commit/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
https://github.com/Knnnk/samplot/blob/92fa27059d9611f7b2cd5bd83f743c6b92f4478e/samplot
https://github.com/Knnnk/samplot/tree/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
Merge pull request #150 from pontushojer/vcf-multithreadhttps://github.com/Knnnk/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
https://github.com/mchowdh200
mchowdh200https://github.com/Knnnk/samplot/commits?author=mchowdh200
4ac4ce0https://github.com/Knnnk/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
https://github.com/Knnnk/samplot/blob/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622/samplot
https://github.com/Knnnk/samplot/tree/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
Merge pull request #151 from pontushojer/rm-optionhttps://github.com/Knnnk/samplot/commit/44b7adeec5604289c9539fee78dd28bffbe96c17
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
44b7adehttps://github.com/Knnnk/samplot/commit/44b7adeec5604289c9539fee78dd28bffbe96c17
https://github.com/Knnnk/samplot/blob/44b7adeec5604289c9539fee78dd28bffbe96c17/samplot
https://github.com/Knnnk/samplot/tree/44b7adeec5604289c9539fee78dd28bffbe96c17
Merge pull request #147 from pontushojer/jitterhttps://github.com/Knnnk/samplot/commit/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
https://github.com/ryanlayer
ryanlayerhttps://github.com/Knnnk/samplot/commits?author=ryanlayer
ebfa497https://github.com/Knnnk/samplot/commit/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
https://github.com/Knnnk/samplot/blob/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c/samplot
https://github.com/Knnnk/samplot/tree/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
Nexthttps://github.com/Knnnk/samplot/commits/master/samplot?after=2929e4a90e5470dc1cb219667606c458b7087265+34
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