thegenemyers / damapper Goto Github PK
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License: Other
Long read to reference genome mapping tool
License: Other
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
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]โ[-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
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