File Changes for markd
switch to commits view, user indexv332_preview to v332_preview2 (2016-04-18 to 2016-05-25) v332
Show details
- src/hg/genePredToFakePsl/genePredToFakePsl.c
- lines changed 6, context: html, text, full: html, text
4e0e5a68eca6f220fc5553949ccfa8b8742bce7c Mon Apr 18 16:05:27 2016 -0700
added note in about case that is not correctly handle
- src/hg/genePredToGtf/genePredToGtf.c
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- lines changed 1, context: html, text, full: html, text
fdef579bae3c23fe4057b74062858bcd60a79209 Mon Apr 18 14:42:07 2016 -0700
removed accidently checked in garbage
- src/hg/lib/genePred.c
- lines changed 5, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/makeDb/outside/gencode/gencodeLoad.mk
- lines changed 3, context: html, text, full: html, text
a7f4d921b739cf892c225997a3d85cea3db25f18 Thu Apr 21 16:20:24 2016 -0700
fixed bug were polyA table wasn't being loaded
- src/hg/makeDb/schema/all.joiner
- lines changed 85, context: html, text, full: html, text
785136193faa141057fdbe9bf48b372c69139e2a Wed Apr 20 11:59:46 2016 -0700
added joiner rules for gencode VM9
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM9.ra
- lines changed 1, context: html, text, full: html, text
48254c04280712ad02cb3184108955fa3736d5fd Tue Apr 19 12:09:19 2016 -0700
fixed incorrect label in mouse GENCODE
- src/hg/mrnaToGene/mrnaToGene.c
- lines changed 45, context: html, text, full: html, text
747563375ea7f3caaaeb7a6d0092706078b0bde9 Mon Apr 18 16:57:33 2016 -0700
simplified the code a bit
- src/hg/mrnaToGene/tests/README
- lines changed 4, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/expected/allCds.gp
- lines changed 21, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/expected/base.gp
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/expected/frame.gp
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/expected/noCds.gp
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/input/base.cds
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/input/base.psl
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/mrnaToGene/tests/makefile
- lines changed 1, context: html, text, full: html, text
a6208b51039416d5be37b79b89d405aeea93be30 Mon Apr 18 13:03:32 2016 -0700
Deal with case were CDS specifications that were create by other
software that didn't correctly set the completeness flags create frames
incorrectly on end-truncated sequences. This code can't possible do the
right thing all the time if completeness isn't correctly flag, however
this makes it more likely to do the right thing when software start from
the beginning of the first coding defining CDS without actually setting
completeness flags.
- src/hg/utils/makefile
- lines changed 1, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- lines changed 2, context: html, text, full: html, text
ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
fixed issues with reverse strand and frame
- src/hg/utils/transMapPslToGenePred/makefile
- lines changed 6, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- src/hg/utils/transMapPslToGenePred/tests/expected/codingFillTest.mapped.gp
- lines changed 33, context: html, text, full: html, text
422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
added gap filling options
- lines changed 1, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 3, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
- src/hg/utils/transMapPslToGenePred/tests/expected/fillTest.mapped.gp
- lines changed 33, context: html, text, full: html, text
422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
added gap filling options
- lines changed 1, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 3, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
- src/hg/utils/transMapPslToGenePred/tests/expected/musTest.mapped.gp
- lines changed 8, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- lines changed 29, context: html, text, full: html, text
ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
fixed issues with reverse strand and frame
- lines changed 1, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 3, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
- src/hg/utils/transMapPslToGenePred/tests/expected/nonCodingFillTest.mapped.gp
- lines changed 33, context: html, text, full: html, text
422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
added gap filling options
- lines changed 1, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 3, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
- src/hg/utils/transMapPslToGenePred/tests/input/musstrain.mapped.psl
- lines changed 17, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- lines changed 38, context: html, text, full: html, text
ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
fixed issues with reverse strand and frame
- lines changed 3, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 3, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
- src/hg/utils/transMapPslToGenePred/tests/input/musstrain.src.gp
- lines changed 17, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- lines changed 33, context: html, text, full: html, text
ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
fixed issues with reverse strand and frame
- lines changed 3, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 4, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
- src/hg/utils/transMapPslToGenePred/tests/makefile
- lines changed 17, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- lines changed 1, context: html, text, full: html, text
ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
fixed issues with reverse strand and frame
- lines changed 16, context: html, text, full: html, text
422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
added gap filling options
- src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
- lines changed 357, context: html, text, full: html, text
3f9ec7598d1179c1802de375f06d01005306b787 Tue Apr 19 20:26:43 2016 -0700
add program to convert transMap PSL to genePred. This handles cds for mappings that start out as genomic annotations (as opposed to alignments)
- lines changed 257, context: html, text, full: html, text
ff922be1fc09d6c561a9c1218e6e75cc96b6162a Wed Apr 20 18:36:55 2016 -0700
fixed issues with reverse strand and frame
- lines changed 31, context: html, text, full: html, text
422619a0907fb407249f54733d875e585bc37c99 Wed Apr 20 20:45:30 2016 -0700
added gap filling options
- lines changed 1, context: html, text, full: html, text
a0a46d43875f54c997ab00b50cdf61e6e9bcc289 Thu Apr 21 11:52:08 2016 -0700
fixed bug with negative strand gene with CDS truncation
- lines changed 6, context: html, text, full: html, text
04d54c90e446a857d692c54652e70f050a6b486b Thu Apr 21 22:52:52 2016 -0700
fixed bug with frame with merging block on negative strand
switch to commits view, user index