Is it necessary to merge all .las file?

[nottwy]

I find that you can use --mlas parameters to avoid load all .las file into memory. It does work!

But I find that I have to merge all .las file. I want to know is it a necessary operaion and can I avoid merge all .las file?

[fxia22]

You don't have to merge all .las files, currently the whole pipeline can work on a block by block basis So you only need to pass --mlas flag and input file prefix abc and it will look for abc.[numbers].las files.

[nottwy]

But in this issue 'https://github.com/HingeAssembler/HINGE/issues/77', the command of 'draft' step is like this: hinge draft --db yeast --las yeast.las --prefix yeast --config nominal.ini --out yeast.draft How to understand this?

[fxia22]

In current version, you can do this instead:

hinge draft --db yeast --las yeast --mlas --prefix yeast --config nominal.ini --out yeast.draft

We will update the manual soon.

[nottwy]

Not only this step, I notice that the DASqv command also needs to be modified. Now it's like this: DASqv -c100 yeast yeast.las But what should I do if I don't have a merged .las file?

[fxia22]

@nottwy you can now use DASqv -c100 yeast yeast.*.las

[nottwy]

Although the 'hinge layout' step supports the --mlas option, it used up to 2 T memory. Is it strange?

[govinda-kamath]

Can you give the exact command you used, and size of your las files?

[nottwy]

1.my command is: hinge layout --db $db --las $las --mlas -x ${prefix} --config $cfg -o xyz 2.I have 95 las files with an average size 8.5G per file. 3.The version of my hinge is: commit aa735993eb737f25b9c442dd71d0889b6ed35e09 Merge: 825432a a9e8582 Author: Fei Xia xf1280@gmail.com Date: Fri Sep 8 13:01:11 2017 -0700

Merge pull request #128 from jameslz/patch-1

add  Boost_INCLUDE_DIR