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Find all significant local alignments between reads
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LAdump: not all trace-points #51

Closed pb-cdunn closed 7 years ago

pb-cdunn commented 7 years ago

It seems that LAdump -t shows the trace-points for the first alignment only.

In fact, LAdump -cd shows all alignements, but LAdump -cdt shows only the first.

E.g.

+ P 3
% P 1
+ T 564
% T 258
@ T 258
P 92772 92773 c .
C 5464 18218 0 12802
T 129
...

Even though it says P3, there are no other sections. And we see only 129 trace-points in the dump, not 564.

Can you verify that?

thegenemyers commented 7 years ago

I reviewed the code for LAdump. Saw a couple of hinky things in there, but none that explained your phenomena. Did clean it up a bit anyway.

Just checked in a version of DALIGNER module where LAmerge uses memmove, daligner now will error exit if the /tmp file area overflows, and with the slight cleanup of LAdump just in case it does fix the problem (although I think not).

If the problem still persists, please send me the data set. Looks small with only 3 overlaps in it.

-- Gene

On 11/17/16, 5:04 PM, Christopher Dunn wrote:

It seems that |LAdump -t| shows the trace-points for the first alignment only.

In fact, |LAdump -cd| shows all alignements, but |LAdump -cdt| shows only the first.

E.g.

|+ P 3 % P 1

  • T 564 % T 258 @ T 258 P 92772 92773 c . C 5464 18218 0 12802 T 129 ... |

Even though it says |P3|, there are no other sections. And we see only |129| trace-points in the dump, not |564|.

Can you verify that?

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