From 25299147202690183cd14f47e298210b3421c82d Mon Sep 17 00:00:00 2001
From: "Michael G. Campana" <campanam@si.edu>
Date: Fri, 13 Sep 2019 13:01:22 -0400
Subject: [PATCH] Gzip handling

---
 CHANGELOG.md |  3 +++
 README.md    |  3 ++-
 vcf2aln.rb   | 16 +++++++++++++++-
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4162d6a..1d1e118 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,9 @@ Michael G. Campana & Jacob A. West-Roberts, 2017-2019
 Smithsonian Conservation Biology Institute  
 Contact: campanam@si.edu  
 
+### Version 0.11.0  
+Read/write gzipped files  
+
 ### Version 0.10.0  
 Probabilistic pseudohaplotype calling  
 Minimum samples called as a percentage option  
diff --git a/README.md b/README.md
index ec615fe..d64618a 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ In the terminal:
 Optionally, vcf2aln.rb can be placed within the user’s $PATH so that it can be executed from any location. Depending on your operating system, you may need to change the shebang line in the script (first line starting with #!) to specify the path of your Ruby executable.  
 
 ## Input  
-vcf2aln requires an all-sites VCF (e.g. such as one produced using EMIT_ALL_SITES in the [Genome Analysis Toolkit](https://software.broadinstitute.org/gatk/)).  
+vcf2aln requires an all-sites VCF (e.g. such as one produced using EMIT_ALL_SITES in the [Genome Analysis Toolkit](https://software.broadinstitute.org/gatk/)). Files with the final extension ".gz" are assumed to be gzip-compressed.  
 
 ## Execution
 Execute the script using `ruby vcf2aln.rb` (or `vcf2aln.rb` if the script is in your $PATH). This will display the help screen. Basic usage is as follows:  
@@ -33,6 +33,7 @@ vcf2aln can also be used in a pipe. For example, it can directly convert the out
 `-i, --input [FILE]`: Input VCF file.  
 `--pipe`: Read data from an uncompressed VCF stream rather than a file.  
 `-o, --outprefix [VALUE]`: Output FASTA alignment prefix.  
+`-z, --gzip`: Gzip output alignments.  
 `-c, --concatenate`: Concatenate markers into single alignment (e.g. concatenate multiple separate chromosomes/contigs).  
 `-s, --skip`: Skip missing sites in VCF.  
 `-O, --onehap`: Print only one haplotype for diploid data. If phasing information is missing, it will generate a pseudohaplotype by randomly assigning one of the alleles. Conflicts with -a.  
diff --git a/vcf2aln.rb b/vcf2aln.rb
index e2bd480..691c65d 100644
--- a/vcf2aln.rb
+++ b/vcf2aln.rb
@@ -2,7 +2,7 @@
 
 #-----------------------------------------------------------------------------------------------
 # vcf2aln
-VCF2ALNVER = "0.10.0"
+VCF2ALNVER = "0.11.0"
 # Michael G. Campana, Jacob A. West-Roberts, 2017-2019
 # Smithsonian Conservation Biology Institute
 #-----------------------------------------------------------------------------------------------
@@ -95,12 +95,16 @@ def print_locus
 			end
 			if $options.alts
 				system("cat *#{$options.outprefix + @name}*.tmp.fa > #{$options.outprefix + @name + '.fa'}")
+				system("gzip #{$options.outprefix + @name + '.fa'}") if $options.gzip
 			else
 				if $options.onehap
 					system("cat *#{$options.outprefix + @name}.tmp.fa > #{$options.outprefix + @name + '.fa'}")
+					system("gzip #{$options.outprefix + @name + '.fa'}") if $options.gzip
 				else
 					system("cat *#{$options.outprefix + @name}.hap1.tmp.fa > #{$options.outprefix + @name + '.hap1.fa'}")
 					system("cat *#{$options.outprefix + @name}.hap2.tmp.fa > #{$options.outprefix + @name + '.hap2.fa'}")
+					system("gzip #{$options.outprefix + @name + '.hap1.fa'}") if $options.gzip
+					system("gzip #{$options.outprefix + @name + '.hap2.fa'}") if $options.gzip
 				end
 			end
 		end
@@ -143,6 +147,7 @@ def self.parse(options)
 		args.adepth = nil #Don't filter allele depth by default
 		args.split_regions = 0 #Don't activate region-split subroutine by default
 		args.write_cycle = 1000000 # Number of cycles before force of write-out
+		args.gzip = false # Gzip output
 		opt_parser = OptionParser.new do |opts|
 			opts.banner = "Command-line usage: ruby vcf2aln.rb [options]"
 			opts.separator ""
@@ -156,6 +161,9 @@ def self.parse(options)
 			opts.on("-o", "--outprefix [VALUE]", String, "Output alignment prefix") do |pref|
 				args.outprefix = pref + "_" if pref != nil
 			end
+			opts.on("-z", "--gzip", "Gzip output alignments") do 
+				args.gzip = true
+			end
 			opts.on("-c", "--concatenate", "Concatenate markers into single alignment") do
 				args.concat = true
 			end
@@ -683,6 +691,12 @@ def read_input
 	regionval = 0
 	if $options.pipe
 		ARGF.each_line { |line| index, previous_index, previous_endex, previous_name, current_locus, prev_pos, write_cycle, region, regionval = vcf_to_alignment(line, index, previous_index, previous_endex, previous_name, current_locus, prev_pos, write_cycle, region, regionval) }
+	elsif $options.infile[-3..-1] == ".gz"
+		Zlib::GzipReader.open($options.infile) do |vcf2aln|
+	 		while line = vcf2aln.gets
+	 			index, previous_index, previous_endex, previous_name, current_locus, prev_pos, write_cycle, region, regionval = vcf_to_alignment(line, index, previous_index, previous_endex, previous_name, current_locus, prev_pos, write_cycle, region, regionval)
+	 		end
+		end
 	else
 		File.open($options.infile, 'r') do |vcf2aln|
 	 		while line = vcf2aln.gets