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Infer ref_clv from chimeric contigs #1

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zyxue opened this issue Jul 10, 2018 · 0 comments
Open

Infer ref_clv from chimeric contigs #1

zyxue opened this issue Jul 10, 2018 · 0 comments
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enhancement New feature or request

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@zyxue
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zyxue commented Jul 10, 2018

Given a chimeric contig, when a bridge read is aligned to the contig, the contig is in one piece; but when the contig is aligned to the genome, it becomes two pieces.

Problem: When looping through the contig to the first-piece, how to infer the genome coord of a clv that's actually aligned the second piece?
@zyxue zyxue added the enhancement New feature or request label Jul 10, 2018
zyxue added a commit that referenced this issue Jul 11, 2018
@zyxue
added contig_is_hardclipped column #1
37f5923
zyxue added a commit that referenced this issue Jul 11, 2018
@zyxue
aggregate contig_is_hardclipped with any after groupby/apply #1
322ad8f
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
get ready for dealing with hardclipped contigs #1
f3a2c79 
updated do_{fwd_rev}_ctg_{lt,rt}_bdg functions to use contig
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_forwad_contig_left_tail_bridge_read_with_left_hard_clip…
ee32619 
…ping #1
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_forwad_contig_left_tail_bridge_read_with_right_hard_cli…
be085c6 
…pping #1
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
made the test case name consistent with the tested function name #1
d99e441
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added harclipping support to do_fwd_ctg_rt_bdg #1
448bf5f 
added test_do_fwd_ctg_rt_bdg_with_left_hardclipping
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_fwd_ctg_rt_bdg_with_right_hardclipping #1
e1e4eec
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_do_fwd_ctg_lt_bdg_with_left_hard_clipping_passing_the_c…
7fa6234 
…tg_clv #1
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_fwd_ctg_lt_bdg_with_right_hard_clipping_passing_the_ctg…
3530d88 
…_clv #1
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added more edgecase tests for do_fwd_ctg_lt_bdg #1
0452da2
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_fwd_ctg_rt_bdg_with_left_hardclipping_passing_ctg_clv #1
7d22c5a
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added test_do_fwd_ctg_rt_bdg_with_right_hardclipping_right_on_ctg_clv #1
bbfd8ee
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
adjusted edgecase tests for do_fwd_ctg_lt_bdg #1
f2fa66a 
to more properly test edge cases.
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
renamed the test file for forward contigs with hardclipping #1
203e884
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
updated & tested do_rev_ctg_lt_bdg for hardclipping #1
dcd9613
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
updated and tested do_rev_ctg_rt_bdg for hardclipping #1
ac21cee
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
added more close-to-edge-case test cases #1
f81bb55 
to test_bridge_forward_contigs_with_hardclipping.py
also renamed some of the test names, trying to be more consistent
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
fixed test_bridge.py for the updated functions #1
01d1ac6
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
factored out calc_hardclips #1
ac92d7a
zyxue added a commit that referenced this issue Jul 13, 2018
@zyxue
factored out do_bridge.py, made the whole thing run #1
a75d662 
to make the whole thing run:
   updated proc.py & evidence/bridge.py for when analyze_bridge returns None
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