| package com.nilshomer.bfx.examples.utilities | |
| import com.fulcrumgenomics.bam.api.SamSource | |
| import com.fulcrumgenomics.cmdline.ClpGroups | |
| import com.fulcrumgenomics.sopt.{arg, clp} | |
| import com.nilshomer.bfx.examples.cmdline.BfxExamplesTool | |
| import com.fulcrumgenomics.commons.CommonsDef.{PathToBam, SafelyClosable} | |
| import com.fulcrumgenomics.util.Io | |
| @clp( |
| package com.nilshomer.bfx.examples.utilities | |
| import com.fulcrumgenomics.cmdline.ClpGroups | |
| import com.fulcrumgenomics.sopt.{arg, clp} | |
| import com.nilshomer.bfx.examples.cmdline.BfxExamplesTool | |
| @clp( | |
| description = "Prints your name to standard out and exits.", | |
| group = ClpGroups.Utilities | |
| ) |
| package com.nilshomer.bfx.examples.utilities | |
| import com.fulcrumgenomics.cmdline.ClpGroups | |
| import com.fulcrumgenomics.sopt.clp | |
| import com.nilshomer.bfx.examples.cmdline.BfxExamplesTool | |
| @clp( | |
| description = "Prints hello world to standard out and exits.", | |
| group = ClpGroups.Utilities | |
| ) |
| # Hello, and welcome to makefile basics. | |
| # | |
| # You will learn why `make` is so great, and why, despite its "weird" syntax, | |
| # it is actually a highly expressive, efficient, and powerful way to build | |
| # programs. | |
| # | |
| # Once you're done here, go to | |
| # http://www.gnu.org/software/make/manual/make.html | |
| # to learn SOOOO much more. |
--input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
For more information on read structures see: https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
The same number of input files and read structures must be provided, with one exception: if supplying exactly 1 or 2 fastq files, both of which are solely template reads, no read structures need be provided.
| /** Performs the unit of work on a resource of type [A] cleaning up the resource in the case of an exception or upon | |
| * completion. | |
| * @param resource the resource upon which work is performed. | |
| * @param cleanup the clean up method to apply to the resource when the work is complete. | |
| * @param doWork the work to perform on the resource, returning a result of type [B]. | |
| * @tparam A the resource type | |
| * @tparam B the result type of the work performed. | |
| * @return Success if the work was performed successfully, Failure otherwise. | |
| */ |
| Unit Tests | Integration Tests | |
|---|---|---|
| Master | GATK | Picard |
| // jeanluc/src/main/scala/dagr/jeanluc/JeanLucMain.scala | |
| /* | |
| * The MIT License | |
| * | |
| * Copyright (c) 2016 Fulcrum Genomics LLC | |
| * | |
| * Permission is hereby granted, free of charge, to any person obtaining a copy | |
| * of this software and associated documentation files (the "Software"), to deal | |
| * in the Software without restriction, including without limitation the rights | |
| * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
| package picard.sam; | |
| import htsjdk.samtools.SAMFileHeader; | |
| import htsjdk.samtools.SAMFileWriter; | |
| import htsjdk.samtools.SAMFileWriterFactory; | |
| import htsjdk.samtools.SAMRecord; | |
| import htsjdk.samtools.SAMSequenceRecord; | |
| import htsjdk.samtools.SamReader; | |
| import htsjdk.samtools.SamReaderFactory; | |
| import htsjdk.samtools.util.CloserUtil; |