René's URL Explorer Experiment


Title: History for samplot/samplot.py - animesh/samplot · GitHub

Open Graph Title: History for samplot/samplot.py - animesh/samplot

X Title: History for samplot/samplot.py - animesh/samplot

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

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

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

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

X: @github

direct link

Domain: github.com

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og:image:altPlot structural variant signals from many BAMs and CRAMs - History for samplot/samplot.py - animesh/samplot
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fixes for python 3.11https://github.com/animesh/samplot/commit/444f3bdde8d74e86173ce6dee824fccfae409371
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https://github.com/animesh/samplot/tree/444f3bdde8d74e86173ce6dee824fccfae409371
Remove `np.int` depreciated in numpy 1.24.0https://github.com/animesh/samplot/commit/44d8685e91885e93f29a96a6e023e232667d03cc
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https://github.com/animesh/samplot/tree/44d8685e91885e93f29a96a6e023e232667d03cc
Merge pull request #183 from pontushojer/jitter-longhttps://github.com/animesh/samplot/commit/db2ba62a68b51cd44faeb18f307561e3f14fbb89
https://github.com/ryanlayer
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https://github.com/animesh/samplot/tree/db2ba62a68b51cd44faeb18f307561e3f14fbb89
Merge pull request #179 from pontushojer/coverage-speeduphttps://github.com/animesh/samplot/commit/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce
https://github.com/ryanlayer
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https://github.com/animesh/samplot/blob/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce/samplot/samplot.py
https://github.com/animesh/samplot/tree/dbf629f2c7d4a23ec9616c0dfc0b32e73ad47bce
Use same offset at both ends of bent line and make the line bends up for large jitter_bounds.https://github.com/animesh/samplot/commit/202b1038e1db985b6ba35554f78e60308ea0278e
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
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https://github.com/animesh/samplot/blob/202b1038e1db985b6ba35554f78e60308ea0278e/samplot/samplot.py
https://github.com/animesh/samplot/tree/202b1038e1db985b6ba35554f78e60308ea0278e
simplify curr_max_insert_size updatehttps://github.com/animesh/samplot/commit/575dc9fcdcdb859c7ec52147fc3aa0fc7aff2d03
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
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https://github.com/animesh/samplot/tree/575dc9fcdcdb859c7ec52147fc3aa0fc7aff2d03
Enable --jitter for long readshttps://github.com/animesh/samplot/commit/ee99ec0c50e2a1c48ee523bd821a3d7a9ad49b16
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
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https://github.com/animesh/samplot/tree/ee99ec0c50e2a1c48ee523bd821a3d7a9ad49b16
fix Missing legend (?) #171. Only include legends for read types that appear in the plot.https://github.com/animesh/samplot/commit/0bed14cf7aa8ee30859058a88d1bfa78d187caa3
https://github.com/pontushojer
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https://github.com/animesh/samplot/tree/0bed14cf7aa8ee30859058a88d1bfa78d187caa3
speed up read coverage collectionhttps://github.com/animesh/samplot/commit/a5a4933a358b895d593246f928ddd1f0660c7a30
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pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
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https://github.com/animesh/samplot/blob/a5a4933a358b895d593246f928ddd1f0660c7a30/samplot/samplot.py
https://github.com/animesh/samplot/tree/a5a4933a358b895d593246f928ddd1f0660c7a30
use logger for messageshttps://github.com/animesh/samplot/commit/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
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https://github.com/animesh/samplot/tree/4a5505fc39fb0503b7293f7f8da3a6648ce90d4e
fix tests and chr prefix strip (#168)https://github.com/animesh/samplot/commit/16560c18bfaf102933c4a7b89e3b28b9230b41d5
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https://github.com/animesh/samplot/tree/16560c18bfaf102933c4a7b89e3b28b9230b41d5
Merge pull request #157 from pontushojer/names-missinghttps://github.com/animesh/samplot/commit/f3968cf7f0412afa156018e747d6d870d718503f
https://github.com/ryanlayer
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Handle case where a gene entry from a GFF is missing the "Name" attribute.https://github.com/animesh/samplot/commit/533c81b7cb368330f74a5c861082583d843cbbd3
https://github.com/pontushojer
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Transcript and exons should end exactly on defined position. Default capstyle project these outside of start/end positionshttps://github.com/animesh/samplot/commit/69209cadd1779b0515edd12fb08b64d34cf87a79
https://github.com/pontushojer
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Move transcript name to top of drawinghttps://github.com/animesh/samplot/commit/091a9e2f17ec69c2e3211caad1e31237aab616e5
https://github.com/pontushojer
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https://github.com/animesh/samplot/tree/091a9e2f17ec69c2e3211caad1e31237aab616e5
Move arrows into transcripts and add multiple throughout transcript at regular intervals.https://github.com/animesh/samplot/commit/d5cc9d60a433c9dec97b441d471d663bd118c0dc
https://github.com/pontushojer
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Unstack overlapping transcriptshttps://github.com/animesh/samplot/commit/fdbdb26fa50d208bc127711a00e8e080a970b448
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typo in help string for jitterhttps://github.com/animesh/samplot/commit/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
92fa270https://github.com/animesh/samplot/commit/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
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Merge pull request #150 from pontushojer/vcf-multithreadhttps://github.com/animesh/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
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Merge pull request #151 from pontushojer/rm-optionhttps://github.com/animesh/samplot/commit/44b7adeec5604289c9539fee78dd28bffbe96c17
https://github.com/ryanlayer
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Merge pull request #147 from pontushojer/jitterhttps://github.com/animesh/samplot/commit/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
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ryanlayerhttps://github.com/animesh/samplot/commits?author=ryanlayer
ebfa497https://github.com/animesh/samplot/commit/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
https://github.com/animesh/samplot/blob/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c/samplot/samplot.py
https://github.com/animesh/samplot/tree/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
Remove unused option `common_insert_size` (fix https://github.com/ryanlayer/samplot/issues/148)https://github.com/animesh/samplot/commit/d2d90e1e4940b48fc96729238b348dbae8b0df2d
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
d2d90e1https://github.com/animesh/samplot/commit/d2d90e1e4940b48fc96729238b348dbae8b0df2d
https://github.com/animesh/samplot/blob/d2d90e1e4940b48fc96729238b348dbae8b0df2d/samplot/samplot.py
https://github.com/animesh/samplot/tree/d2d90e1e4940b48fc96729238b348dbae8b0df2d
Jitter also for linked readshttps://github.com/animesh/samplot/commit/e22744a3610540b07b1f2ba54b0eab259487899f
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
e22744ahttps://github.com/animesh/samplot/commit/e22744a3610540b07b1f2ba54b0eab259487899f
https://github.com/animesh/samplot/blob/e22744a3610540b07b1f2ba54b0eab259487899f/samplot/samplot.py
https://github.com/animesh/samplot/tree/e22744a3610540b07b1f2ba54b0eab259487899f
Add argument --jitter to add jitter to insert sizes.https://github.com/animesh/samplot/commit/92580e1da3b2f14884f552b4fba295a27c600c80
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
92580e1https://github.com/animesh/samplot/commit/92580e1da3b2f14884f552b4fba295a27c600c80
https://github.com/animesh/samplot/blob/92580e1da3b2f14884f552b4fba295a27c600c80/samplot/samplot.py
https://github.com/animesh/samplot/tree/92580e1da3b2f14884f552b4fba295a27c600c80
Enable plot generation without using subprocesshttps://github.com/animesh/samplot/commit/b96a1f9304a2887f93a73baf82b163864b097c7f
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
b96a1f9https://github.com/animesh/samplot/commit/b96a1f9304a2887f93a73baf82b163864b097c7f
https://github.com/animesh/samplot/blob/b96a1f9304a2887f93a73baf82b163864b097c7f/samplot/samplot.py
https://github.com/animesh/samplot/tree/b96a1f9304a2887f93a73baf82b163864b097c7f
Jitter lines in y-dim to avoid overlapshttps://github.com/animesh/samplot/commit/982f60a025974d6bda7c645d7897ae4b6a1db2ac
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
982f60ahttps://github.com/animesh/samplot/commit/982f60a025974d6bda7c645d7897ae4b6a1db2ac
https://github.com/animesh/samplot/blob/982f60a025974d6bda7c645d7897ae4b6a1db2ac/samplot/samplot.py
https://github.com/animesh/samplot/tree/982f60a025974d6bda7c645d7897ae4b6a1db2ac
Remove unused functions identified with (vulture)[https://github.com/jendrikseipp/vulture]https://github.com/animesh/samplot/commit/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
https://github.com/pontushojer
pontushojerhttps://github.com/animesh/samplot/commits?author=pontushojer
b7f650ahttps://github.com/animesh/samplot/commit/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
https://github.com/animesh/samplot/blob/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835/samplot/samplot.py
https://github.com/animesh/samplot/tree/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
Allow manual scaling of annotation track size and other fixes (#141)https://github.com/animesh/samplot/commit/a1c1342930ae433e6f9672b3226a2bc22283389b
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
a1c1342https://github.com/animesh/samplot/commit/a1c1342930ae433e6f9672b3226a2bc22283389b
https://github.com/animesh/samplot/blob/a1c1342930ae433e6f9672b3226a2bc22283389b/samplot/samplot.py
https://github.com/animesh/samplot/tree/a1c1342930ae433e6f9672b3226a2bc22283389b
generalized exception handling for tabixhttps://github.com/animesh/samplot/commit/43043121ee454157dd1d47daebb3a5dd49c69cb2
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
4304312https://github.com/animesh/samplot/commit/43043121ee454157dd1d47daebb3a5dd49c69cb2
https://github.com/animesh/samplot/blob/43043121ee454157dd1d47daebb3a5dd49c69cb2/samplot/samplot.py
https://github.com/animesh/samplot/tree/43043121ee454157dd1d47daebb3a5dd49c69cb2
enabled csi indices for annotation fileshttps://github.com/animesh/samplot/commit/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
94b1c1chttps://github.com/animesh/samplot/commit/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0
https://github.com/animesh/samplot/blob/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0/samplot/samplot.py
https://github.com/animesh/samplot/tree/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0
remove offset/sci notation from tickshttps://github.com/animesh/samplot/commit/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
bbe4041https://github.com/animesh/samplot/commit/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c
https://github.com/animesh/samplot/blob/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c/samplot/samplot.py
https://github.com/animesh/samplot/tree/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c
fixed minor break in same_yaxis_scales from last commithttps://github.com/animesh/samplot/commit/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
e1b2f28https://github.com/animesh/samplot/commit/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34
https://github.com/animesh/samplot/blob/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34/samplot/samplot.py
https://github.com/animesh/samplot/tree/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34
created max coverage optionhttps://github.com/animesh/samplot/commit/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
8e52ca9https://github.com/animesh/samplot/commit/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c
https://github.com/animesh/samplot/blob/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c/samplot/samplot.py
https://github.com/animesh/samplot/tree/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c
added catch for Nonetype and changed gff to gff3 explicitlyhttps://github.com/animesh/samplot/commit/8fcf78bd3e84382e6f30882d29119adfce4f9eda
https://github.com/jbelyeu
jbelyeuhttps://github.com/animesh/samplot/commits?author=jbelyeu
8fcf78bhttps://github.com/animesh/samplot/commit/8fcf78bd3e84382e6f30882d29119adfce4f9eda
https://github.com/animesh/samplot/blob/8fcf78bd3e84382e6f30882d29119adfce4f9eda/samplot/samplot.py
https://github.com/animesh/samplot/tree/8fcf78bd3e84382e6f30882d29119adfce4f9eda
Nexthttps://github.com/animesh/samplot/commits/master/samplot/samplot.py?after=2929e4a90e5470dc1cb219667606c458b7087265+34
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