Some code to (partially) read in a reference panel

do you know where I can download stu for mac? I’d like to have one available on my personal computer.

(if I google stu, its not clear what is the software)

On 28 Mar 2017, at 22:24, aaronmcdaid notifications@github.com wrote:

To compile this, you'll need to wonder stu program, a replacment for Make.

I've compiled stu and it's on the master at

/data/sgg2/aaron/shared/AgingPipeline.March28/stu

I haven't tested it very thouroughly on hpc1, no idea if it will work. If there is a compilation problem, please send the error messages.

If it does compile ("Build successful"), then run

bin/ssimp --raw.ref YOURvcfFILE.vcf

It still doesn't do anything interesting, but it's a start

You can view, comment on, or merge this pull request online at:

https://github.com/sinarueeger/ssimp_software/pull/1 https://github.com/sinarueeger/ssimp_software/pull/1 Commit Summary

Aaron's first commit here. Starting on a basic C++ program. First step is to read a reference panel start using getopt_long src/other/DIE.hh Split out into a 'options' module 'ssimp' is now a module on its own 'bin/o/LIST_OF_HH_FILES' and fix up 'options' a little Correctly read in '--raw.ref' argument. Not yet doing anything with it though bring in 'other/PP.hh Start a 'file.reading' module Aaron's crazy FWD trick More in @clean make a 'src' subdir inside 'fwd'. Note, this doesn't compile FWD(namespace), not just FWD. Still doing nested namespace wrong FWD() namespace issue fixed Suppress that warning bin.stu: Fix the problem with multiple FWDs in one file Skip the '##' and print the header Count the possible delimiters Return the delimiter that is present -Werror for 'amcdaid' only split out all the headers tokenize() (late) src/other/utils.hh PP(vector) LIST_OF_HH_FILES shouldn't include the src/fwd headers bin/o/LIST_OF_HH_FILES -> bin/LIST_OF_HH_FILES offset_and_name for all nine VCF files DIE.hh: WARNING operator= to allow only one assignment Use all fields, not just the first 20 Some defaulted constructors Store the field names that are unaccounted for, which is probably the subject names Delete that 'checker' stuff, not actually interesting A few things around reading in more of the (vcf) file pure virtual =0; Populate a member for 'each_SNP_and_its_offset' and return it Store the underlying file name too utils.hh: No need for that newline there. utils:: lexical_cast Use lexical_cast to parse the chromosome and position to ints Sort by chr:pos. (and print a bit less) File Changes

A bin.stu https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-0 (98) A main.stu https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-1 (10) A src/file.reading.cc https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-2 (261) A src/file.reading.hh https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-3 (15) A src/options.cc https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-4 (36) A src/options.hh https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-5 (9) A src/other/DIE.hh https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-6 (8) A src/other/PP.hh https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-7 (32) A src/other/utils.hh https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-8 (40) A src/ssimp.cc https://github.com/sinarueeger/ssimp_software/pull/1/files#diff-9 (21) Patch Links:

https://github.com/sinarueeger/ssimp_software/pull/1.patch https://github.com/sinarueeger/ssimp_software/pull/1.patch https://github.com/sinarueeger/ssimp_software/pull/1.diff https://github.com/sinarueeger/ssimp_software/pull/1.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/sinarueeger/ssimp_software/pull/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AEP5RiOhAqpMw86ffjlkJaLKxdnqd53lks5rqWx8gaJpZM4MsJbb.

zkutalik / ssimp_software

Some code to (partially) read in a reference panel #1