0000000000000000000000000000000000000000 6402131ecf8c43ba7e03db4f7e1d942617508e55 SLAment <SLAment@users.noreply.github.com> 1576239710 +0100	commit (initial): .gitignore - added a file to ignore stuff that are not relevant
6402131ecf8c43ba7e03db4f7e1d942617508e55 da83cb9d9ae9d2f7bbff272b3af9e0208ee7eb17 SLAment <SLAment@users.noreply.github.com> 1576239782 +0100	commit: Added the Snakemake pipelines for analyses done in the Spok block paper
da83cb9d9ae9d2f7bbff272b3af9e0208ee7eb17 5d3a4fd53e0edca002aeb95fa191eb46b29f53d9 SLAment <SLAment@users.noreply.github.com> 1576249633 +0100	commit: Added a general README for the repo
5d3a4fd53e0edca002aeb95fa191eb46b29f53d9 31ae96de40471fc1c5a25c0ced543a8dae8bd563 SLAment <SLAment@users.noreply.github.com> 1581934197 +0100	commit: I fixed a few typos
31ae96de40471fc1c5a25c0ced543a8dae8bd563 102e69a0779b7f2dafeeb7eb273f25be364994f9 SLAment <SLAment@users.noreply.github.com> 1581934314 +0100	commit: I added the pipeline PaAnnotation.smk that produces gene models with MAKER and also repeat annotation with RepeatMasker
102e69a0779b7f2dafeeb7eb273f25be364994f9 ceab5d56abc1ace1cd6321aac04ec4e2b13d06bb SLAment <SLAment@users.noreply.github.com> 1581935737 +0100	pull origin master: Merge made by the 'recursive' strategy.
ceab5d56abc1ace1cd6321aac04ec4e2b13d06bb de8b115e44dcd85728c190471ad8b9ae7417db05 SLAment <SLAment@users.noreply.github.com> 1581937605 +0100	commit: I added the rulegraph.png figure for PaTEs.smk and cleaned a bit
de8b115e44dcd85728c190471ad8b9ae7417db05 ebc16ca8dc60336ec936be970ff643cd2ec4f6e8 SLAment <SLAment@users.noreply.github.com> 1581937756 +0100	commit: Show the rulegraph
ebc16ca8dc60336ec936be970ff643cd2ec4f6e8 ec64ad5f59372d36a2bf80728cb6bf30780f7569 SLAment <SLAment@users.noreply.github.com> 1581937839 +0100	commit: Add rulegraph.png
ec64ad5f59372d36a2bf80728cb6bf30780f7569 1f3335ba5c3b43d46fba37fc3780a4c212d19e7c SLAment <SLAment@users.noreply.github.com> 1581937942 +0100	commit: rename README for Annotation
1f3335ba5c3b43d46fba37fc3780a4c212d19e7c bf419a8e911cd5d94c765628d801900659999f30 SLAment <SLAment@users.noreply.github.com> 1581938446 +0100	commit: I added the configuration file text explicitly in the README
bf419a8e911cd5d94c765628d801900659999f30 ecd75e656350fae788b95fa9760815b9462346b9 SLAment <SLAment@users.noreply.github.com> 1581938496 +0100	commit: Ups, TMI
ecd75e656350fae788b95fa9760815b9462346b9 38c74d986a4c8ea15ab4c7d27589ed863e1575bc SLAment <SLAment@users.noreply.github.com> 1581938699 +0100	commit: Trying to use subscripts
38c74d986a4c8ea15ab4c7d27589ed863e1575bc deb513103f4e9379f5aae5a79e459b6f550af98e SLAment <SLAment@users.noreply.github.com> 1581941104 +0100	commit: Cleaning
deb513103f4e9379f5aae5a79e459b6f550af98e cfaab85ae5e17493e802736baaf30008c99f975a SLAment <SLAment@users.noreply.github.com> 1581951378 +0100	commit: Remove snakemake logs
cfaab85ae5e17493e802736baaf30008c99f975a b839f4a887584182967e8fe697711e7f761cee28 SLAment <SLAment@users.noreply.github.com> 1581951436 +0100	commit: Added .snakemake to the gitignore file
b839f4a887584182967e8fe697711e7f761cee28 b8ad2385a82dd7295d7585adbb6bf4bdf8f5da15 SLAment <SLAment@users.noreply.github.com> 1581951621 +0100	commit: Removing snakemake logs
b8ad2385a82dd7295d7585adbb6bf4bdf8f5da15 fc307fc5f3ea2011a87395e980813873d522b79b SLAment <SLAment@users.noreply.github.com> 1582030674 +0100	commit: Changed to slightly darker green for alignments
fc307fc5f3ea2011a87395e980813873d522b79b 6b4a5a841c77f76ce3c4b00dd3b80036559b95a8 SLAment <SLAment@users.noreply.github.com> 1582030707 +0100	commit: Made green darker and now the Spok block is a bit closer to center of Circos
6b4a5a841c77f76ce3c4b00dd3b80036559b95a8 1ed69d3fa41f510f761938f098d824b30b2f98a4 SLAment <SLAment@users.noreply.github.com> 1582030724 +0100	commit: Added Chekof and Scoty
1ed69d3fa41f510f761938f098d824b30b2f98a4 e83716e5f86a2385663a55946ff2285470f82f3a SLAment <SLAment@users.noreply.github.com> 1582030731 +0100	commit: Added Chekof and Scoty
e83716e5f86a2385663a55946ff2285470f82f3a bf38342f97c1e9b3c6ab1e73a3402fe7a2a7159c SLAment <SLAment@users.noreply.github.com> 1585232956 +0100	commit: Updated the title and link for bioRxiv
bf38342f97c1e9b3c6ab1e73a3402fe7a2a7159c 9e75fed7d609a396c2fe2e481b08f970a9b5825b SLAment <SLAment@users.noreply.github.com> 1585233023 +0100	commit: Updated the title and link for bioRxiv
9e75fed7d609a396c2fe2e481b08f970a9b5825b 7e031c75900fd3019df890327713ab6e0a8852c8 SLAment <SLAment@users.noreply.github.com> 1585233049 +0100	commit: Updated the title and link for bioRxiv
7e031c75900fd3019df890327713ab6e0a8852c8 37d512567254d57fe9b32026d5f27de379b644ed SLAment <SLAment@users.noreply.github.com> 1585838271 +0200	commit: Updated the link to the Suh Lab scripts
37d512567254d57fe9b32026d5f27de379b644ed 8da8a2961344b6f949cfd7daad7e8458eac88b0d SLAment <sandra.ament@evobio.eu> 1587471242 +0200	commit: Fixed small mistakes in comments
8da8a2961344b6f949cfd7daad7e8458eac88b0d b80356bb1fa7f53717cb1c2c52ce0e84717b074a SLAment <SLAment@users.noreply.github.com> 1592498733 +0200	commit: Updated links to Alex Suh' scripts
b80356bb1fa7f53717cb1c2c52ce0e84717b074a e2301c927667888c19aef61ab3f39552cf093710 SLAment <SLAment@users.noreply.github.com> 1601055718 +0200	commit: Made the Wa137 block slightly larger, changed the conservation track to blue to make it more visable, and updated the coordinates of the block tracks
e2301c927667888c19aef61ab3f39552cf093710 c814b06f59a81266caa560b51df74c5638debcbb SLAment <SLAment@users.noreply.github.com> 1601055733 +0200	commit: Made the Wa137 block slightly larger, changed the conservation track to blue to make it more visable, and updated the coordinates of the block tracks
c814b06f59a81266caa560b51df74c5638debcbb fd2da3038e8f9a8a7a8a8a328cd5a99fcdddd141 SLAment <sandra.ament@evobio.eu> 1603216257 +0200	commit: Added actual scripts needed for the Annotation Pipeline, and for calculating total repeat coverage
fd2da3038e8f9a8a7a8a8a328cd5a99fcdddd141 56f37d9f54b4d489df3334e4bdeee0459c822a24 SLAment <sandra.ament@evobio.eu> 1603216389 +0200	commit: Added actual scripts needed for the Annotation Pipeline, and for calculating total repeat coverage
56f37d9f54b4d489df3334e4bdeee0459c822a24 d13a27515c481913efefb97c8929b32cc5dd6b38 SLAment <SLAment@users.noreply.github.com> 1603383634 +0200	commit: A pipeline to calculate the distribution of k-mers (substring) of length six in the genome(s) of Podospora species using Jellyfish
d13a27515c481913efefb97c8929b32cc5dd6b38 c5dbbee63f3fa01eda45e56068b3eb55670c5412 SLAment <SLAment@users.noreply.github.com> 1603383691 +0200	commit: Renamed README
c5dbbee63f3fa01eda45e56068b3eb55670c5412 7a8d4df790d58f69039b8eedc7f55ca94fc54aff SLAment <SLAment@users.noreply.github.com> 1603383764 +0200	commit: Changes title README
7a8d4df790d58f69039b8eedc7f55ca94fc54aff 95183cb0da138375e6de46ac7248a9b37e558ee2 SLAment <SLAment@users.noreply.github.com> 1603383793 +0200	commit: Added italics to title
95183cb0da138375e6de46ac7248a9b37e558ee2 e76ace5278e68db0582e0776809cb09d010f5da2 SLAment <SLAment@users.noreply.github.com> 1603383847 +0200	commit: Fixed display of results figure
e76ace5278e68db0582e0776809cb09d010f5da2 2a137f073e63ae911483e6dbac3be9770b9c70fa SLAment <SLAment@users.noreply.github.com> 1603383995 +0200	commit: Added description of configuration file
2a137f073e63ae911483e6dbac3be9770b9c70fa 985e2b12f822cd7d0c9ceaea257cbd160942dbe1 SLAment <SLAment@users.noreply.github.com> 1603384054 +0200	commit: TMI
985e2b12f822cd7d0c9ceaea257cbd160942dbe1 e86e00372d2dbff544d6f2004028eb7a4de241e7 SLAment <SLAment@users.noreply.github.com> 1603384101 +0200	commit: Added a line about Unix
e86e00372d2dbff544d6f2004028eb7a4de241e7 cbc83bba5cd1095bd78706b623b02d04cb985b47 SLAment <sandra.ament@evobio.eu> 1603404945 +0200	commit: Updating title of pipelin
cbc83bba5cd1095bd78706b623b02d04cb985b47 6f2693d6bf1bf486350cac7da24d18f321b8eea2 SLAment <sandra.ament@evobio.eu> 1603459504 +0200	commit: I changed the regex I was using to color the genes orange or purple, now is more precise
6f2693d6bf1bf486350cac7da24d18f321b8eea2 db8689c8ae00828806eb264b9bf498fdcf919524 SLAment <sandra.ament@evobio.eu> 1603459602 +0200	commit: I fixed some errors with the previous annotation
db8689c8ae00828806eb264b9bf498fdcf919524 29b2349894167de50a4c9b1030c81c8ee2d4cb32 SLAment <sandra.ament@evobio.eu> 1603462012 +0200	commit: Improved name of gff in config files
29b2349894167de50a4c9b1030c81c8ee2d4cb32 9fa748abbbf4f2d4e3ab0924b3ac7fd3ca2f1660 SLAment <sandra.ament@evobio.eu> 1603462039 +0200	commit: I had forgotten to change the name of the mRNA of one Uhera
9fa748abbbf4f2d4e3ab0924b3ac7fd3ca2f1660 73f70d29c41778d275c04fe4003a3ff426a083cb SLAment <sandra.ament@evobio.eu> 1603462077 +0200	commit: Improved name of gff
73f70d29c41778d275c04fe4003a3ff426a083cb 738b551d576500546e9bd99462f02461ca26eba7 SLAment <sandra.ament@evobio.eu> 1603462172 +0200	commit: Improved name of gff
738b551d576500546e9bd99462f02461ca26eba7 bdcb5f149aefc282adcd8d2c0f4908b7e3c93f9e SLAment <sandra.ament@evobio.eu> 1603462259 +0200	commit: Fixed comments about GFFslicer.py
bdcb5f149aefc282adcd8d2c0f4908b7e3c93f9e fa1d829662b0a4f361297eff5799eb0c1f0aa5d9 SLAment <sandra.ament@evobio.eu> 1603812951 +0100	commit: I changed the regex I was using to color the genes orange or purple
fa1d829662b0a4f361297eff5799eb0c1f0aa5d9 0f1573dfd01ac8fcc05bb8e2ede52646130ec665 SLAment <sandra.ament@evobio.eu> 1603813176 +0100	commit: Changed the names of the annotations files
0f1573dfd01ac8fcc05bb8e2ede52646130ec665 dd45a6e106fa9079de42dedfa6fa3ace20bffb83 SLAment <sandra.ament@evobio.eu> 1603813271 +0100	commit: I changed the names of annotation files and fixed the config description
dd45a6e106fa9079de42dedfa6fa3ace20bffb83 ed89c2ed45c5c10a9f35782690342becefe9249a SLAment <sandra.ament@evobio.eu> 1603813414 +0100	commit: Fixed the annotation files to something decent
ed89c2ed45c5c10a9f35782690342becefe9249a e6195f35b61b4871853767dfb098f95ed7bcbc16 SLAment <sandra.ament@evobio.eu> 1603816673 +0100	commit: Fixed several issues with Wa137 annotation, but they have small effect on the results. Just a few genes are orange now
e6195f35b61b4871853767dfb098f95ed7bcbc16 1d473e605b68a0f8eadd64c752fc5e0f39848cd8 SLAment <sandra.ament@evobio.eu> 1603816909 +0100	commit: Removed snakemake log that shouldn't be there
1d473e605b68a0f8eadd64c752fc5e0f39848cd8 fab7c7b7f73a150d217e56a76abaa9d6dea39ea7 SLAment <SLAment@users.noreply.github.com> 1603913587 +0100	commit: Changed Chekof3 to Chekof_fragment in Wa28s gff
