René's URL Explorer Experiment


Title: History for samplot - ryanlayer/samplot · GitHub

Open Graph Title: History for samplot - ryanlayer/samplot

X Title: History for samplot - ryanlayer/samplot

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

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

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

Opengraph URL: https://github.com/ryanlayer/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 - ryanlayer/samplot
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samplothttps://github.com/ryanlayer/samplot/commits/stix-prototype/samplot
stix-prototypehttps://github.com/ryanlayer/samplot/tree/stix-prototype
fixed zoom interval plotting for bedpe.https://github.com/ryanlayer/samplot/commit/ca3cf29121c120f7f3f286c225cd686421454109
https://github.com/mchowdh200
mchowdh200https://github.com/ryanlayer/samplot/commits?author=mchowdh200
ca3cf29https://github.com/ryanlayer/samplot/commit/ca3cf29121c120f7f3f286c225cd686421454109
https://github.com/ryanlayer/samplot/blob/ca3cf29121c120f7f3f286c225cd686421454109/samplot
https://github.com/ryanlayer/samplot/tree/ca3cf29121c120f7f3f286c225cd686421454109
got bedpe plotting working at a basic level.https://github.com/ryanlayer/samplot/commit/95d510e00dc3d25bf901700d153511986c3695b0
https://github.com/mchowdh200
mchowdh200https://github.com/ryanlayer/samplot/commits?author=mchowdh200
95d510ehttps://github.com/ryanlayer/samplot/commit/95d510e00dc3d25bf901700d153511986c3695b0
https://github.com/ryanlayer/samplot/blob/95d510e00dc3d25bf901700d153511986c3695b0/samplot
https://github.com/ryanlayer/samplot/tree/95d510e00dc3d25bf901700d153511986c3695b0
ran Black formatting toolhttps://github.com/ryanlayer/samplot/commit/a429019b329fee33646f6d883bec6d10f91c87b9
https://github.com/mchowdh200
mchowdh200https://github.com/ryanlayer/samplot/commits?author=mchowdh200
a429019https://github.com/ryanlayer/samplot/commit/a429019b329fee33646f6d883bec6d10f91c87b9
https://github.com/ryanlayer/samplot/blob/a429019b329fee33646f6d883bec6d10f91c87b9/samplot
https://github.com/ryanlayer/samplot/tree/a429019b329fee33646f6d883bec6d10f91c87b9
add bedpe plotter. TODO: testhttps://github.com/ryanlayer/samplot/commit/664a96f446d23fbec868996b551e41aad58a4b49
https://github.com/mchowdh200
mchowdh200https://github.com/ryanlayer/samplot/commits?author=mchowdh200
664a96fhttps://github.com/ryanlayer/samplot/commit/664a96f446d23fbec868996b551e41aad58a4b49
https://github.com/ryanlayer/samplot/blob/664a96f446d23fbec868996b551e41aad58a4b49/samplot
https://github.com/ryanlayer/samplot/tree/664a96f446d23fbec868996b551e41aad58a4b49
Merge pull request #157 from pontushojer/names-missinghttps://github.com/ryanlayer/samplot/commit/f3968cf7f0412afa156018e747d6d870d718503f
https://github.com/ryanlayer
ryanlayerhttps://github.com/ryanlayer/samplot/commits?author=ryanlayer
f3968cfhttps://github.com/ryanlayer/samplot/commit/f3968cf7f0412afa156018e747d6d870d718503f
https://github.com/ryanlayer/samplot/blob/f3968cf7f0412afa156018e747d6d870d718503f/samplot
https://github.com/ryanlayer/samplot/tree/f3968cf7f0412afa156018e747d6d870d718503f
Handle case where a gene entry from a GFF is missing the "Name" attribute.https://github.com/ryanlayer/samplot/commit/533c81b7cb368330f74a5c861082583d843cbbd3
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
533c81bhttps://github.com/ryanlayer/samplot/commit/533c81b7cb368330f74a5c861082583d843cbbd3
https://github.com/ryanlayer/samplot/blob/533c81b7cb368330f74a5c861082583d843cbbd3/samplot
https://github.com/ryanlayer/samplot/tree/533c81b7cb368330f74a5c861082583d843cbbd3
Transcript and exons should end exactly on defined position. Default capstyle project these outside of start/end positionshttps://github.com/ryanlayer/samplot/commit/69209cadd1779b0515edd12fb08b64d34cf87a79
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
69209cahttps://github.com/ryanlayer/samplot/commit/69209cadd1779b0515edd12fb08b64d34cf87a79
https://github.com/ryanlayer/samplot/blob/69209cadd1779b0515edd12fb08b64d34cf87a79/samplot
https://github.com/ryanlayer/samplot/tree/69209cadd1779b0515edd12fb08b64d34cf87a79
Move transcript name to top of drawinghttps://github.com/ryanlayer/samplot/commit/091a9e2f17ec69c2e3211caad1e31237aab616e5
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
091a9e2https://github.com/ryanlayer/samplot/commit/091a9e2f17ec69c2e3211caad1e31237aab616e5
https://github.com/ryanlayer/samplot/blob/091a9e2f17ec69c2e3211caad1e31237aab616e5/samplot
https://github.com/ryanlayer/samplot/tree/091a9e2f17ec69c2e3211caad1e31237aab616e5
Move arrows into transcripts and add multiple throughout transcript at regular intervals.https://github.com/ryanlayer/samplot/commit/d5cc9d60a433c9dec97b441d471d663bd118c0dc
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
d5cc9d6https://github.com/ryanlayer/samplot/commit/d5cc9d60a433c9dec97b441d471d663bd118c0dc
https://github.com/ryanlayer/samplot/blob/d5cc9d60a433c9dec97b441d471d663bd118c0dc/samplot
https://github.com/ryanlayer/samplot/tree/d5cc9d60a433c9dec97b441d471d663bd118c0dc
Unstack overlapping transcriptshttps://github.com/ryanlayer/samplot/commit/fdbdb26fa50d208bc127711a00e8e080a970b448
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
fdbdb26https://github.com/ryanlayer/samplot/commit/fdbdb26fa50d208bc127711a00e8e080a970b448
https://github.com/ryanlayer/samplot/blob/fdbdb26fa50d208bc127711a00e8e080a970b448/samplot
https://github.com/ryanlayer/samplot/tree/fdbdb26fa50d208bc127711a00e8e080a970b448
typo in help string for jitterhttps://github.com/ryanlayer/samplot/commit/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
92fa270https://github.com/ryanlayer/samplot/commit/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
https://github.com/ryanlayer/samplot/blob/92fa27059d9611f7b2cd5bd83f743c6b92f4478e/samplot
https://github.com/ryanlayer/samplot/tree/92fa27059d9611f7b2cd5bd83f743c6b92f4478e
Merge pull request #150 from pontushojer/vcf-multithreadhttps://github.com/ryanlayer/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
https://github.com/mchowdh200
mchowdh200https://github.com/ryanlayer/samplot/commits?author=mchowdh200
4ac4ce0https://github.com/ryanlayer/samplot/commit/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
https://github.com/ryanlayer/samplot/blob/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622/samplot
https://github.com/ryanlayer/samplot/tree/4ac4ce0976a6db6e6a9b38d4c48b3f99a3654622
Merge pull request #151 from pontushojer/rm-optionhttps://github.com/ryanlayer/samplot/commit/44b7adeec5604289c9539fee78dd28bffbe96c17
https://github.com/ryanlayer
ryanlayerhttps://github.com/ryanlayer/samplot/commits?author=ryanlayer
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https://github.com/ryanlayer/samplot/blob/44b7adeec5604289c9539fee78dd28bffbe96c17/samplot
https://github.com/ryanlayer/samplot/tree/44b7adeec5604289c9539fee78dd28bffbe96c17
Merge pull request #147 from pontushojer/jitterhttps://github.com/ryanlayer/samplot/commit/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
https://github.com/ryanlayer
ryanlayerhttps://github.com/ryanlayer/samplot/commits?author=ryanlayer
ebfa497https://github.com/ryanlayer/samplot/commit/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
https://github.com/ryanlayer/samplot/blob/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c/samplot
https://github.com/ryanlayer/samplot/tree/ebfa497dc7140adbd2bf8fbab6c2ef6e6b4a6a9c
Remove unused option `common_insert_size` (fix https://github.com/ryanlayer/samplot/issues/148)https://github.com/ryanlayer/samplot/commit/d2d90e1e4940b48fc96729238b348dbae8b0df2d
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
d2d90e1https://github.com/ryanlayer/samplot/commit/d2d90e1e4940b48fc96729238b348dbae8b0df2d
https://github.com/ryanlayer/samplot/blob/d2d90e1e4940b48fc96729238b348dbae8b0df2d/samplot
https://github.com/ryanlayer/samplot/tree/d2d90e1e4940b48fc96729238b348dbae8b0df2d
Jitter also for linked readshttps://github.com/ryanlayer/samplot/commit/e22744a3610540b07b1f2ba54b0eab259487899f
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
e22744ahttps://github.com/ryanlayer/samplot/commit/e22744a3610540b07b1f2ba54b0eab259487899f
https://github.com/ryanlayer/samplot/blob/e22744a3610540b07b1f2ba54b0eab259487899f/samplot
https://github.com/ryanlayer/samplot/tree/e22744a3610540b07b1f2ba54b0eab259487899f
Add argument --jitter to add jitter to insert sizes.https://github.com/ryanlayer/samplot/commit/92580e1da3b2f14884f552b4fba295a27c600c80
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
92580e1https://github.com/ryanlayer/samplot/commit/92580e1da3b2f14884f552b4fba295a27c600c80
https://github.com/ryanlayer/samplot/blob/92580e1da3b2f14884f552b4fba295a27c600c80/samplot
https://github.com/ryanlayer/samplot/tree/92580e1da3b2f14884f552b4fba295a27c600c80
Enable multithread plotting from VCFhttps://github.com/ryanlayer/samplot/commit/152031a81cf4d572721c9cdf4515acb569ea8b4f
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
152031ahttps://github.com/ryanlayer/samplot/commit/152031a81cf4d572721c9cdf4515acb569ea8b4f
https://github.com/ryanlayer/samplot/blob/152031a81cf4d572721c9cdf4515acb569ea8b4f/samplot
https://github.com/ryanlayer/samplot/tree/152031a81cf4d572721c9cdf4515acb569ea8b4f
Enable plot generation without using subprocesshttps://github.com/ryanlayer/samplot/commit/b96a1f9304a2887f93a73baf82b163864b097c7f
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
b96a1f9https://github.com/ryanlayer/samplot/commit/b96a1f9304a2887f93a73baf82b163864b097c7f
https://github.com/ryanlayer/samplot/blob/b96a1f9304a2887f93a73baf82b163864b097c7f/samplot
https://github.com/ryanlayer/samplot/tree/b96a1f9304a2887f93a73baf82b163864b097c7f
Jitter lines in y-dim to avoid overlapshttps://github.com/ryanlayer/samplot/commit/982f60a025974d6bda7c645d7897ae4b6a1db2ac
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
982f60ahttps://github.com/ryanlayer/samplot/commit/982f60a025974d6bda7c645d7897ae4b6a1db2ac
https://github.com/ryanlayer/samplot/blob/982f60a025974d6bda7c645d7897ae4b6a1db2ac/samplot
https://github.com/ryanlayer/samplot/tree/982f60a025974d6bda7c645d7897ae4b6a1db2ac
Remove unused functions identified with (vulture)[https://github.com/jendrikseipp/vulture]https://github.com/ryanlayer/samplot/commit/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
https://github.com/pontushojer
pontushojerhttps://github.com/ryanlayer/samplot/commits?author=pontushojer
b7f650ahttps://github.com/ryanlayer/samplot/commit/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
https://github.com/ryanlayer/samplot/blob/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835/samplot
https://github.com/ryanlayer/samplot/tree/b7f650ad28c0dd36f9d7d07e9ff05223f4b88835
add bump to v 1.3.0 (#142)https://github.com/ryanlayer/samplot/commit/905ce04aac979f2b4ce553751435836621009140
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
905ce04https://github.com/ryanlayer/samplot/commit/905ce04aac979f2b4ce553751435836621009140
https://github.com/ryanlayer/samplot/blob/905ce04aac979f2b4ce553751435836621009140/samplot
https://github.com/ryanlayer/samplot/tree/905ce04aac979f2b4ce553751435836621009140
Allow manual scaling of annotation track size and other fixes (#141)https://github.com/ryanlayer/samplot/commit/a1c1342930ae433e6f9672b3226a2bc22283389b
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
a1c1342https://github.com/ryanlayer/samplot/commit/a1c1342930ae433e6f9672b3226a2bc22283389b
https://github.com/ryanlayer/samplot/blob/a1c1342930ae433e6f9672b3226a2bc22283389b/samplot
https://github.com/ryanlayer/samplot/tree/a1c1342930ae433e6f9672b3226a2bc22283389b
generalized exception handling for tabixhttps://github.com/ryanlayer/samplot/commit/43043121ee454157dd1d47daebb3a5dd49c69cb2
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
4304312https://github.com/ryanlayer/samplot/commit/43043121ee454157dd1d47daebb3a5dd49c69cb2
https://github.com/ryanlayer/samplot/blob/43043121ee454157dd1d47daebb3a5dd49c69cb2/samplot
https://github.com/ryanlayer/samplot/tree/43043121ee454157dd1d47daebb3a5dd49c69cb2
enabled csi indices for annotation fileshttps://github.com/ryanlayer/samplot/commit/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
94b1c1chttps://github.com/ryanlayer/samplot/commit/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0
https://github.com/ryanlayer/samplot/blob/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0/samplot
https://github.com/ryanlayer/samplot/tree/94b1c1c4626196c7c2b4004cc388bd94cc63b7f0
version bumphttps://github.com/ryanlayer/samplot/commit/8bef03d788981b6ddd35fc27ec9dc9d004a61e68
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
8bef03dhttps://github.com/ryanlayer/samplot/commit/8bef03d788981b6ddd35fc27ec9dc9d004a61e68
https://github.com/ryanlayer/samplot/blob/8bef03d788981b6ddd35fc27ec9dc9d004a61e68/samplot
https://github.com/ryanlayer/samplot/tree/8bef03d788981b6ddd35fc27ec9dc9d004a61e68
remove offset/sci notation from tickshttps://github.com/ryanlayer/samplot/commit/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
bbe4041https://github.com/ryanlayer/samplot/commit/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c
https://github.com/ryanlayer/samplot/blob/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c/samplot
https://github.com/ryanlayer/samplot/tree/bbe4041cf2f4e9ac0b8499b737a5ddbde79e130c
fixed minor break in same_yaxis_scales from last commithttps://github.com/ryanlayer/samplot/commit/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
e1b2f28https://github.com/ryanlayer/samplot/commit/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34
https://github.com/ryanlayer/samplot/blob/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34/samplot
https://github.com/ryanlayer/samplot/tree/e1b2f28dd1af529f9c7cf1ad1071f4623c3b8b34
created max coverage optionhttps://github.com/ryanlayer/samplot/commit/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
8e52ca9https://github.com/ryanlayer/samplot/commit/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c
https://github.com/ryanlayer/samplot/blob/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c/samplot
https://github.com/ryanlayer/samplot/tree/8e52ca991794909bffdef8b6b6cc4bfd9674cf8c
changed gff to gff3https://github.com/ryanlayer/samplot/commit/3a94779bd744928e4758d4c53f62a0010698da97
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
3a94779https://github.com/ryanlayer/samplot/commit/3a94779bd744928e4758d4c53f62a0010698da97
https://github.com/ryanlayer/samplot/blob/3a94779bd744928e4758d4c53f62a0010698da97/samplot
https://github.com/ryanlayer/samplot/tree/3a94779bd744928e4758d4c53f62a0010698da97
removed unset FORMAT fields and changed gff to gff3 explicitlyhttps://github.com/ryanlayer/samplot/commit/eadc0934a3450b67ac2faa75be9e716c4b5e8174
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
eadc093https://github.com/ryanlayer/samplot/commit/eadc0934a3450b67ac2faa75be9e716c4b5e8174
https://github.com/ryanlayer/samplot/blob/eadc0934a3450b67ac2faa75be9e716c4b5e8174/samplot
https://github.com/ryanlayer/samplot/tree/eadc0934a3450b67ac2faa75be9e716c4b5e8174
added catch for Nonetype and changed gff to gff3 explicitlyhttps://github.com/ryanlayer/samplot/commit/8fcf78bd3e84382e6f30882d29119adfce4f9eda
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
8fcf78bhttps://github.com/ryanlayer/samplot/commit/8fcf78bd3e84382e6f30882d29119adfce4f9eda
https://github.com/ryanlayer/samplot/blob/8fcf78bd3e84382e6f30882d29119adfce4f9eda/samplot
https://github.com/ryanlayer/samplot/tree/8fcf78bd3e84382e6f30882d29119adfce4f9eda
added test for vcf with gff3/bed fileshttps://github.com/ryanlayer/samplot/commit/b8bc46353fab47010b35eae6b223d01a66424bfe
https://github.com/jbelyeu
jbelyeuhttps://github.com/ryanlayer/samplot/commits?author=jbelyeu
b8bc463https://github.com/ryanlayer/samplot/commit/b8bc46353fab47010b35eae6b223d01a66424bfe
https://github.com/ryanlayer/samplot/blob/b8bc46353fab47010b35eae6b223d01a66424bfe/samplot
https://github.com/ryanlayer/samplot/tree/b8bc46353fab47010b35eae6b223d01a66424bfe
bumps micro versionhttps://github.com/ryanlayer/samplot/commit/2c5b8ae1f95c0cb97958f9a04f2455f89f9884d8
2c5b8aehttps://github.com/ryanlayer/samplot/commit/2c5b8ae1f95c0cb97958f9a04f2455f89f9884d8
https://github.com/ryanlayer/samplot/blob/2c5b8ae1f95c0cb97958f9a04f2455f89f9884d8/samplot
https://github.com/ryanlayer/samplot/tree/2c5b8ae1f95c0cb97958f9a04f2455f89f9884d8
removes get_overlap bughttps://github.com/ryanlayer/samplot/commit/3ecad660da84a0bf5f8ea6c464f016ba66be0a84
3ecad66https://github.com/ryanlayer/samplot/commit/3ecad660da84a0bf5f8ea6c464f016ba66be0a84
https://github.com/ryanlayer/samplot/blob/3ecad660da84a0bf5f8ea6c464f016ba66be0a84/samplot
https://github.com/ryanlayer/samplot/tree/3ecad660da84a0bf5f8ea6c464f016ba66be0a84
Nexthttps://github.com/ryanlayer/samplot/commits/stix-prototype/samplot?after=ca3cf29121c120f7f3f286c225cd686421454109+34
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