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Hi, Gene~
I get las file now,so want to convert las to sam file to do next analysis.

Thanks~
Si

Is the hash symbol in

https://github.com/thegenemyers/DAMAPPER/blob/master/damapper.c#L840

intentional?

In map.c line 2595 (see https://github.com/thegenemyers/DAMAPPER/blob/master/map.c#L2595 ) there is

part = Malloc(sizeof(Zones *)*COmax,"Allocating zones vector");

which I think should be

part = Malloc(sizeof(Zones)*COmax,"Allocating zones vector");

as part is of type Zones * .

Could you please check?

Thanks
German

In commit 3a4c0c7 you introduced a unchecked call to free in
DB.c. In damapper it might be called with an argument of record->alen = 0xffffffffffffffff which, of course, leads to a segfault. I am not sure where the value originates but it is always the same value.

hi,Myers. I map an bacteria draft genome to the complete genome with DAMAPPER ,when use LAshow -a to see the .las file,an error occured:
LAshow: Index out of bounds (Load_Read)

thanks~

In the latest version damapper will produce an error if using a .dam and .db file as DBs. The error looks like:

damapper: Could not open DB ./reference.1.db

It originates from DB.c:531. The reason for the error is an unintended reassignment of isdam at damapper.c:826.

Hi!
I have a reference.fasta file. How to get ref:db|dam?

(damapper [-vbpCN] [-k<int(20)>] [-t] [-M] [-T<int(4)>]
[-e<double(.85)] [-s<int(100)>] [-n<double(1.)>]
[-m]+ ref:db|dam reads:db|dam ...)

I split query.db to 10 blocks, ref.db to 4 blocks,then use "HPC.daligner -T2 -e.8 rer query 1-10 >run.job.sh", but run.jobs.sh file contain "rm query.1.ref.1 query.1.ref.2 query.1.ref.3 query.1.ref.4",
should be "rm query.1.ref.1.las query.1.ref.2.las query.1.ref.3.las query.1.ref.4.las" ?

thanks~

Hello,
I'm trying out DAMAPPER for mapping a set of unitigs to PacBio reads, and when parsing the results I notice that sometimes duplicate alignments to different parts of the same read are reported as chains, which seems like not the intended behavior. Perhaps this has to do with the fact that I'm aligning short sequences to long reads, and not vice versa? Here's an example from the LAdump -lc output:

P 6661 109492 n >
L 83 12383
C 0 83 11853 11937
P 6661 109492 n -
L 83 12383
C 0 83 11948 12032

Here, the query contig '83' aligned fully to two locations on read '109492', which should probably be reported as two separate LAs, and not as a chain.

Eugene G