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I tried to build the package on GCC 7.3.0 (default compiler on CentOS7) and got the build failure below. It looks like the C++ 11 syntax needs to be explicitly enabled on this version of GCC, so could this be added to the makefile for a smoother proceedure for CentOS users?
make.log

Hi.
Installing FASTQuick in conda env failed in make test step.
cmake did not complain about missing libraries.

Conda environment has the following packages installed:
cmake 3.14.0 ; make 4.2.1 ; zlib 1.2.11 ; bzip2 1.0.8; backports.lzma 0.0.14 ; openssl 1.1.1g ; libcurl 7.69.1 ; htslib 1.10.2
SO: Ubuntu 18.04

Maybe I am missing some prerequisite?
Thanks

Hello there,
I used the dataset provided in the package to test the tool and once I tried to run the Rscript to generate the plots, it throws the following error:
[1] "Usage:Rscript RPlotScript.R <output_prefix> <SVDPrefix> <FASTQuickInstallDir>" Warning message: In regularize.values(x, y, ties, missing(ties)) : collapsing to unique 'x' values Warning message: In regularize.values(x, y, ties, missing(ties)) : collapsing to unique 'x' values Error in pivot:1 : argument of length 0 Calls: findBump Execution halted

I used the following command to invoke the Rscript:
Rscript RPlotScript.R test_out hapmap_3.3.b37.dat ${FASTQuick}

note that I have put hapmap_3.3.b37.dat files in the same directory as output files.
Thank you in advance.

Hi,

I am interested in the tool, but find parts of the documentation somewhat confusing.

Could you maybe clarify the difference between these options:

--siteVCF
--candidateVCF
--predefinedVCF
--dbSNP
--dbsnpVCF
--SVDPrefix
--RefVCF
--RefVCFList

And the difference between:
--callableRegion
and
--regionList

siteVCF (for candidate sites in the wiki) and predefinedVCF (for predefined sites) are used in the index function, so I assume they contain the SNPs to build the reduced region as written in the paper, which is also filtered by either callableRegion and regionList, but what exactly is the difference between candidates and predefined sites and what is the difference between target region and callable region?

In the main Readme file you use dbSNP, in the wiki you have dbsnpVCF as option. Is that a type or are there two options. If there is only one option, how is this VCF file handled differently from the candidate or predefined sites?

Also in the examples the candidateVCF option is used, which is not found in the wiki.
The same goes for RefVCFList.

I would appreciate if you could take the time explain what the each option does.

The index step of FASTQuick appears to call out to a tabix binary (I believe that happens here: https://github.com/Griffan/FASTQuick/blob/master/src/RefBuilder.cpp#L342). It doesn't appear to be documented that this is required. Also, I'm not sure what version of tabix supports the -R option being passed. The standard one installed by apt on ubuntu results in an invalid option error:

FASTQuick index --siteVCF hapmap.test.vcf.gz --dbsnpVCF dbsnp.test.vcf.gz --ref test.fa --out_index_prefix NA12878

The following parameters are available.  Ones with "[]" are in effect:

Available Options
                   Input/Output Files : --siteVCF [hapmap.test.vcf.gz],
                                        --dbsnpVCF [dbsnp.test.vcf.gz],
                                        --ref [test.fa],
                                        --out_index_prefix [NA12878],
                                        --mask [Empty]
   Parameters for Reference Sequence  : --var_long [1000], --var_short [9000],
                                        --flank_len [250],
                                        --flank_long_len [1000]


NOTICE - Initializing Rolling Hash Table with size: 536870912 bytes in 3321 sec

NOTICE - Index file doesn't exist, building...

NOTICE - Initialization of RefBwt...

NOTICE - Loading Ref fai file done!

tabix: invalid option -- 'R'
[tabix] the index file either does not exist or is older than the vcf file. Please reindex.

WARNING -
Building dbsnp subset.vcf failed!