"Missing" edges

[fbemm]

Hi,

the seqwish GFA seems to miss some edges for loops:

P 4 34+,32-,32-,32-,344- # only a part of the path S 32 G L 32 + 32 + OM L 32 + 32 + OM L 32 + 32 - OM L 32 - 32 + OM

Should'nt there be a:

L 32 - 32 - OM

Works otherwise pretty great!

F

[ekg]

Has this been resolved? I was using vg view -Fv to detect when this happens. I needed to add a mutex lock on a shared bitvector. Without it this tended to happen.

On Thu, Oct 25, 2018, 11:47 Felix Bemm notifications@github.com wrote:

Hi,

the seqwish GFA seems to miss some edges for loops:

P 4 34+,32-,32-,32-,344- # only a part of the path S 32 G L 32 + 32 + OM L 32 + 32 + OM L 32 + 32 - OM L 32 - 32 + OM

Should'nt there be a:

L 32 - 32 - OM

Works otherwise pretty great!

F

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[fbemm]

Testing with the latest commit atm. I keep you updated.

[fbemm]

Getting a core dump right now for a data set that worked before. Digging..

*** Error in `seqwish': free(): invalid next size (normal): 0x0000152ac00009f0 ***
======= Backtrace: =========
[0x56ecd1]
[0x5779c6]
[0x57b9f7]
[0x53bfe9]
[0x4843be]
[0x484510]
[0x539544]
[0x53cf0c]
[0x53aa2a]
[0x548485]
[0x5bc719]

[fbemm]

The GFA file now contains when debugging switched on:

St1_2.1 974421  890470  899546  +       St1_2.69        206126  126841  135687  5185    9098    0       cg:Z:
St1_2.1 974421  0       5649    +       St1_2.272       329270  323592  329254  4873    5675    0       cg:Z:

[fbemm]

I am not able to run seqwish on the above mentioned data set any more, and can't trace the reason for the segfault either. Switching back to an earlier release works (f75121a3b50a436ef394bb94d8672af69ae1545f).

[fbemm]

Switching from Ubuntu 16.04 to 18.04 solved the segfaults.

[ekg]

That's great! Can you work with the output graph?

On Thu, Jan 31, 2019, 10:42 Felix Bemm <notifications@github.com wrote:

Switching from Ubuntu 16.04 to 18.04 solved the segfaults.

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[fbemm]

One thing that might be problematic is that quite a number of links are simply duplicated. Currently testing if removing them solves the "duplicated rank" problem I always run into when indexing with vg. But otherwise it looks fine. I will report back in case I discover further challenges.

[ekg]

That's interesting, and shouldn't happen. Can you find the duplicate L records in the output GFA?

On Thu, Jan 31, 2019, 13:11 Felix Bemm <notifications@github.com wrote:

One thing that might be problematic is, that quite a number of links are simply duplicated. Currently testing if that solves the "duplicated rank" problem I always run into when indexing with vg.

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[fbemm]

Yes. Just an example:

L       1504    +       34338705        -       OM
L       1504    +       1505    +       OM
L       1504    +       1505    +       OM
L       1505    +       1506    +       OM

Using a brute force sort it's about 3/4 of my links are actually duplicated exactly 2 times.

In this particular case it's 15,850,483 out of 65,419,141 links that are unique, the rest is present 2 times.

[fbemm]

This somehow disappeared.