diff --git a/doc/wiki b/doc/wiki index 0e6af64fd9..44c0fe6b4f 160000 --- a/doc/wiki +++ b/doc/wiki @@ -1 +1 @@ -Subproject commit 0e6af64fd9759153d2178d10e6004ef49092c75f +Subproject commit 44c0fe6b4ff67f46c05f833e104781b63262e51a diff --git a/test/longread/annotations.gff3 b/test/longread/annotations.gff3 new file mode 100644 index 0000000000..f998bc72ee --- /dev/null +++ b/test/longread/annotations.gff3 @@ -0,0 +1,4 @@ +CHM13#0#chr1 Liftoff gene 10 1000 . + . gene_name=FakeGene;Name=FakeGene +CHM13#0#chr1 Liftoff transcript 10 100 . + . gene_name=FakeGene;Name=FakeGene;transcript_id=FakeTranscript +CHM13#0#chr1 Liftoff exon 20 200 . + . gene_name=FakeGene;Name=FakeGene;Parent=FakeTranscript;ID=exon:FakeTranscript:0 +CHM13#0#chr1 Liftoff exon 500 1000 . + . gene_name=FakeGene;Name=FakeGene;Parent=FakeTranscript;ID=exon:FakeTranscript:1 diff --git a/test/longread/kinnex.fq b/test/longread/kinnex.fq new file mode 100644 index 0000000000..6ec78bf684 --- /dev/null +++ b/test/longread/kinnex.fq @@ -0,0 +1,4 @@ +@S20_13790 +TGACTATGCTATTGGTTTATGTATTTACTATACTGTATCATTATTATTTTAGATCAGACATTTTCTATTTATTTTTTAAAAAGCTAACTGTAAAACAGCCTCAGACAGGTCCTTCAGGAGGTATCCCAGCAGAAGACACTGTTAACACAGGAGATGACAGCTCCGTGTGTTACTGCCTTCCCAGTGACATAATGCGGAGGTGGAAGATAGTGATATTGATGATCCTGACCCTGTATAGGCCTAGACTAATATGTGTGTTTTTGTTTCCGTTTTTAACCAAAAAAAAAAAAAAAAAAAGTTTAAGTAAAAATAAATTTTTTTAAAAAAGAAAAAAGCATATAGAATTAGAATATAAAAAAAGAAAATATTTTTGTGCAACAATATCTTCATGTTTTAAACTAAGCGTTATTACAAAAAAGTCAAATAAGTTTTTAAAAATTAAAAAAATTACAAAGTAAAAAAGTTCCAGTAAGCTAAAGATTAATTTACACACTGTAAATTTGTGTCCTGTATGATTTTTTATGTTTTATACTGTATTTTACTATGTTCAGTATGCTTAGATACACAGATACACAATTGTGTCACATCTGCCTGCTGCATTCAGTACAGTAACATGCTGCACAAGTTTGTAGCCTAGGAGCAATAGGCTATACCATATAGGCTAGATGTGCAGTAGTCACTATCATCTTGGTCTGTTTGAGTACACTCTAGGATGGCTGCACAACAATGAAATTGCCAAACACATTTCTGGAGTGCAAAACTCAGTATCTAGAGGAAGTATTTTAAGTATTAATGGTATTTAACATTTCTCAGAACATCACACCCCATCCTTCAACAACACATGACTATATATAATGCAAACACTAGTCAAAAGAAAGCCAAGTAGCTATATTAATATAAAACAAAGACATCAAAAAAAGAACTGCCTAGCATAGAGGGACATAACGCAATAATAAAAGGATCAAATCACCACTAAGATCTAAAAGTCCTAAATATGTATGCACCTACCACCAGAGCTTCAAAACACATACAGCAAAACCAATACAAGTGGAAAGAAAAATAGACAAATCCACAATAGCAACTGAAGACTTCAAAACTCTCAGCCCACTGTCACCCTGTTACTCGACATAGTACTGGAAGTCCTAGCTAGAGCTATCGGACAAGAGAAACATATAGGGGGAATCCAAATTGGAAAGGAAATAATCAAATTATCTTTGTTTGCTGATGATACGAACGTATATTTGCAAAAACCTAAAGATTTCACAAGAAAACTATTAGAACTGATCAATTCAGTAGTTGCAGGATACAAAATCAACATACAAAAATAAGTAGCATTTCTATATGCCAACAGTAAACACTGTGAAAAAGAAATTTTAAAAGTAATCCCATTTACAATAGCCACACATAAAATTAAATACCTAGGAATTAACTTCACCGAAGAAGTGAAAGATCTCTATGATGAAAACTATAAAACACTGATGAAGGCAATTGAAGGATACCAAAAAATGAAAAAATATTCCATGTACATGGATTGGAAAAATCAATATTGTTAAAATGTCCATACTACCCAAAGCAATCTACAGATTCAATGCAATCCCTATCGAAATACCAATGACATTCTTCACAGAAATAGAAAAAACAATCTGAAAATTTATATGAAACTACAAAAGACCCAGAATAGTTACAGCTATCCTAAGCAAAAAGAACAAAACTGGAGGAATCACATTACCTAACTTCAAATTATACTGCAGAGCTATAGTAACCAAAACAGCAAGTTACTGGCATAAAAACAGACACATAGACCAATGGACCAGAATAGAGAACCCAGAAACAAAATCCACACATCTATGGTGAACTTGTTTTTGACAAAGGTGCCAAGAACATATACTGGGGAAAAGACAGTCTTTTCATAAATGGTGCTGGGAAAACTGGATATCCATATGCAGAAGAATGAAAATAGACTCCTATCTCTCACTGTCTACAAAAATCAAATTAAAACA ++ +~Z~~~~LO~~~Z~~~~U~~~~~M~~~~~~~~~~~~J~~Y~~~~~~~~~V~~~T~~~~~L~~~Q~~~~~~~~~~~~~~P~L~~~V~~~~~X~~~~~~~~~~~~~~|~~~U~~~~~M~~~~~ZE~~~~~~~~~~~~~~~~~~~~~~~_~~~~|~~~T~~~~~~~~~N~~~~M~~~~~~~~~~D~~~~~~~~~J~~~~~{~~~~~Z~~W~~~~~V~~~~Z~~~~~~~~~T~~~~Q~~~~~~B~~~~~~~~~~~~~~~~~H~~~~~~~~~~U~~~~C~~~`~~~~J~~~~~~~~~~J~~~~~~A~~~}~~~~~Q~~~~0~~~~~~^~~~L~~~~~~E~~~~M~~Y~~I~~~~~~~Y~~T~~~~~~S~NP~M~M~|~~L~~~~U~]~~~~~E~~~~~~I~~~~~O~Z~{~J~~~~W~~~~~}~~~~1~~~~~~~~~~~~~~~N~~~~W~~~~~~~~~~~~~~~~~~Y~~~~~~~I~~~`~~~~X~~~~~~~~~~~~~W~~~~O~~~~~~U~~K~~Q~U~~~~~~~~G~~~~W~~:~~~B~~~~=~D~R~~~~~~~~~]~~~L~~~~O~Z~~~V~~^~~~~~M~~~~~~~~L~~~~~1~~~~L~~~~V~Y~~~Y~F~~~~Q~~~J~~~~~~~~~~~~~~~R~~~~~~~~S~~~~~~~{~~}~~~~~{~~\~~D~A~~~~~~`~~~~V~Y~~~^~~~C~~~~~V~~~Z~~~~~~~~~~~~S~~~~]~Y~~~~~~C~~~~~{~~~~[~~~~U~D~~~~G~~~~~~}~~~P~Z~~A~~~~~~~X~~~Q~UW~~~~~~~~~~~H~{~C~~~~~~~~~~}~~~~~~~~~~R~~~~~~~~~~~~~~~}~~~~~~Q~H~~~Z~A~~~~~N~~J~~~~M~O~~~Q~~~~~~M~~~|~~~~~~W~~~~L~~H~~~~~~|~~W~V~~~\~~~~~~~~|~~~~S~~H~~M~~{~F~~~G~~~Q~~~~[~~~X~~~BE~~~~~~S~~~~~}~~~~~~~~~K~~~~P~~~~~Y~~~~H~~~~~~~~~~^~~~V~~~~~~~~Y~~~4~~~LKD~~~~~M~~N~~V~~N~~~~~~~~~~~~~Y~~~RZ~~~B~~~Z~~~Y~~~~~~N~~P~~|N~~~~A~~~~~~~~~{~IF~~~&~~J~~~~~I~~~~Q~U~~~~~~~Z~~~~S~~~F~~I~/~~~~~8~~~~~~~~~~~~~~~~~~~~~J~~~~~~~ET~~?~~~~~~M~~~~O~~B~~~K~~~L~~~~~~~~~D~~~SF~~~~J~V~~~~~~~~~|~~T~E~~[~~V~~~~~~~~~~V~~~~~~~~~~D~~~~~~~~~~~~~~`(~~~~~~U~V~~Z~~L~~_~X~~~~~~~~~X~~~~Y}~|~~~S~}~~~~~|~~~~~N~~~~~~~~~~~~~~~~~~~~~~Z~~W~~X~~H~~O~~~J~~~~~~~~~~~X~~~S~~K~~~~~~~~~~~~~~~~~~~~T~~~Z~~~O~US~R~KD~~~Q~~]~~~~~~~I~~~{~{~~~M~~~F~~~~~~~~~N~~~~~S~~~H~D~~F~NJ~~~Z~~~_~~~~~~~~~~[~U~~QW~~~I~~~]~~~~~~~~~~~~~~~~ZL~~~~~~~~{~K~~~R~~~~O~~~~~~~~~~B~~M~~~`~~~~~~~~~~~~~~~Y~~~F~~~J~~~~{S~~~T~~~~`~~~~~W~~~~~M~~~~~Z~~~U~~~T~~~~~~~S~~~~~~~~~~~~~~~V~~~W~~~~~~|~~~~~L~|~~~X~|~~~~A~M~[~~P~~E~~~~~~~U~~~T~~~V~~~I~~~~~~~P~~~~~~~~~~~L~~~~~~~~~~~~~'~{[~~~~~~~~~W~WZ~*~~|~~[H*Z~~K~~I~~~QLS~|~~~T~~~~~~~Z~~O~&~~~~~~~*<=~Z~~%`~)S[~~~~~~]~~OJTB~~JN~~~~~~U~~~R~~~H~~~~~{~~N~P~~~D~~:~~~3&^\~~|SQ?~28~U~~~R~~~~~S.~ITCY8%~XV~~~+NL~L~~`~C~D~~TMAE@|~$IM~F~~|~~~~\~~~O~~~~T~~~~~~X~~~