mculinovic / eagler Goto Github PK

Switch from manual temporary files to something like tmpnam.

The current configuration does not allow multiple instances of the scaffolder to run in the same folder.

It seems, graphmap have some problem with "align" flag. How to fix it ?

➜ bin git:(master) ✗ ~/Tools/EAGLER/release/eagler -x ont -t 40 /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/EAGLER_SSPACED_out -g graphmap
[INPUT] Reading draft genome: /media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta
[INPUT] Reading long reads: /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta
[ALIGNER] Initializing graphmap aligner...
[ALIGNER] Creating index...
ERROR: Unknown value of 'tool' parameter. Exiting.

Usage:
graphmap tool

Options
tool STR Specifies the tool to run:
align - the entire GraphMap pipeline.
owler - Overlapping With Long Erroneous Reads.

../vendor/seqan/include/seqan/basic/basic_exception.h:368 FAILED! (Uncaught exception of type std::runtime_error: command "graphmap -v 0 -I -r "/media/urbe/TOSHIBALAB/falconUnzip/SSPACED_P2/scaffolds.fasta"" failed with exit status 256)
[1] 46760 abort (core dumped) ~/Tools/EAGLER/release/eagler -x ont -t 40 -g graphmap

Edit Makefile.rules such that it recompiles all source files that depend on the edited header file.

Align reads to all contigs at the same time with one bwa command, with intent to reduce false positive alignments.

Automatically detect concurrency level and set BWA flag.

Fix linker error on -lrt flag on OS X. Find a way do discriminate OS in makefile rules.

Realign dropped reads to contig when coverage falls below acceptable value.

Rework SeqAn submodule configuration to avoid pulling the whole repository when installing the ONTscaffolder. Only the include folder should be used.

Program creates multiple temporary files during execution. They should be stored in temporary folder.
Also, figure out a best way to handle temporary file paths in code.

Add doxygen documentation support.

Create a script to automatically test various implementations and parameters of the scaffolder.

• circular genome trim should use anchor alignment for trimming
• add support for scaffold merge
• add support for reverse complement contigs
• support for multiple scaffolds

List of small enhancements that need to be done:

• change default make target to build only release version
• make install should copy executable to /usr/local/bin
• add make remove to amend make install
• advanced OSX compiler detection
• add -t THREADS option to set the concurrency level manually
• add option for setting the expected maximum size of the gap
• use only one command line argument as prefix for all output files

1. add (x-) syntax option to reference a fragment till the end of the reference genome
2. add -k option to invert the cut/keep output

Input parameters: pairs (start, end)
Meaning: remove genome subsequence [start, end] from reference genome