Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Reinjected sequences on matches containing inserts are invalid according to samtools #109

Closed
unode opened this issue Jun 6, 2019 · 0 comments · Fixed by #111
Closed

Reinjected sequences on matches containing inserts are invalid according to samtools #109

unode opened this issue Jun 6, 2019 · 0 comments · Fixed by #111

Comments

@unode
Copy link
Member

unode commented Jun 6, 2019

The issue is captured in the test-case added in 1068e29.

It basically boils down to samtools considering I in CIGAR strings to add to the length of the sequence. As such a CIGAR 5M1I5M is considered to have length 11 while current code calculates 10 due to ignoring I in:

ngless/NGLess/Data/Sam.hs

Line 195 in 1068e29

matchSize' includeSoft cigar

unode added a commit that referenced this issue Jun 7, 2019
@unode
TST+BUG Fix CIGAR size calculation for inserts
cb4283b 
closes #109
unode added a commit that referenced this issue Jun 7, 2019
@unode
TST+BUG Fix CIGAR size calculation for insertions
05af241 
closes #109
@unode unode mentioned this issue Jun 7, 2019
Merged
unode added a commit that referenced this issue Jun 7, 2019
@unode
TST+BUG Fix CIGAR size calculation for insertions
2652e5f 
closes #109
unode added a commit that referenced this issue Jun 7, 2019
@unode
TST+BUG Fix CIGAR size calculation for insertions
31a4648 
closes #109
luispedro pushed a commit that referenced this issue Jun 14, 2019
@unode @luispedro
TST+BUG Fix CIGAR size calculation for insertions
0e5e9e8 
closes #109
luispedro added a commit that referenced this issue Jan 20, 2020
@luispedro
RLS Version 1.1.0
75de5a7 
Many changes to the language and the internal code warrant a new
release:

Full ChangeLog
	* Fix CIGAR interpretation (#109) occurring when I is present
	* Call bwa mem so that it behaves in a deterministic way (independently of
	the number of threads used)
	* Add `include_fragments` option to orf_find
	* Add early check for column headers in `count()`
	* Add ``sense`` argument to `count()`
	* Add line numbers to FastQ parsing errors
	* Fix __extra_args argument in map()
	* Add `discard_singles` function
	* Add `interleaved` option to fastq()
	* `load_mocat_sample` now fails if `pair.2` exists but `pair.1` doesn't
	* Reintroduce zstd compression (after fixes upstream)
luispedro added a commit that referenced this issue Jan 22, 2020
@luispedro
RLS Version 1.1.0
f96cf31 
Many changes to the language and the internal code warrant a new
release:

Full ChangeLog
	* Fix CIGAR interpretation (#109) occurring when I is present
	* Call bwa mem so that it behaves in a deterministic way (independently of
	the number of threads used)
	* Add `include_fragments` option to orf_find
	* Add early check for column headers in `count()`
	* Add ``sense`` argument to `count()`
	* Add line numbers to FastQ parsing errors
	* Fix __extra_args argument in map()
	* Add `discard_singles` function
	* Add `interleaved` option to fastq()
	* `load_mocat_sample` now fails if `pair.2` exists but `pair.1` doesn't
	* Reintroduce zstd compression (after fixes upstream)
luispedro added a commit that referenced this issue Feb 1, 2020
@luispedro
RLS Version 1.1.0
84e6c4a 
Many changes to the language and the internal code warrant a new
release:

Full ChangeLog
	* Fix CIGAR interpretation (#109) occurring when I is present
	* Call bwa mem so that it behaves in a deterministic way (independently of
	the number of threads used)
	* Add `include_fragments` option to orf_find
	* Add early check for column headers in `count()`
	* Add ``sense`` argument to `count()`
	* Add line numbers to FastQ parsing errors
	* Fix __extra_args argument in map()
	* Add `discard_singles` function
	* Add `interleaved` option to fastq()
	* `load_mocat_sample` now fails if `pair.2` exists but `pair.1` doesn't
	* Reintroduce zstd compression (after fixes upstream)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Fix CIGAR size calculation for insertions ngless-toolkit/ngless
1 participant
@unode