From: martinahansen Date: Thu, 27 Oct 2011 13:06:45 +0000 (+0000) Subject: removed biopieces find_mids remove_mids read_solexa X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=f5c05822d4d64cac55aefe7d670b2e4092b553d9;p=biopieces.git removed biopieces find_mids remove_mids read_solexa git-svn-id: http://biopieces.googlecode.com/svn/trunk@1602 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/find_mids b/bp_bin/find_mids deleted file mode 100755 index 52da69e..0000000 --- a/bp_bin/find_mids +++ /dev/null @@ -1,114 +0,0 @@ -#!/usr/bin/env ruby - -# Copyright (C) 2007-2010 Martin A. Hansen. - -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License -# as published by the Free Software Foundation; either version 2 -# of the License, or (at your option) any later version. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - -# http://www.gnu.org/copyleft/gpl.html - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - -# This program is part of the Biopieces framework (www.biopieces.org). - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - -# Find and count MID tags in sequences in the stream. - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -require 'maasha/biopieces' - -MID_LEN = 10 - -mids = %w{ ACGAGTGCGT ACGCTCGACA AGACGCACTC AGCACTGTAG ATCAGACACG - ATATCGCGAG CGTGTCTCTA CTCGCGTGTC TAGTATCAGC TCTCTATGCG - TGATACGTCT TACTGAGCTA CATAGTAGTG CGAGAGATAC ATACGACGTA - TCACGTACTA CGTCTAGTAC TCTACGTAGC TGTACTACTC ACGACTACAG - CGTAGACTAG TACGAGTATG TACTCTCGTG TAGAGACGAG TCGTCGCTCG - ACATACGCGT ACGCGAGTAT ACTACTATGT ACTGTACAGT AGACTATACT - AGCGTCGTCT AGTACGCTAT ATAGAGTACT CACGCTACGT CAGTAGACGT - CGACGTGACT TACACACACT TACACGTGAT TACAGATCGT TACGCTGTCT - TAGTGTAGAT TCGATCACGT TCGCACTAGT TCTAGCGACT TCTATACTAT - TGACGTATGT TGTGAGTAGT ACAGTATATA ACGCGATCGA ACTAGCAGTA - AGCTCACGTA AGTATACATA AGTCGAGAGA AGTGCTACGA CGATCGTATA - CGCAGTACGA CGCGTATACA CGTACAGTCA CGTACTCAGA CTACGCTCTA - CTATAGCGTA TACGTCATCA TAGTCGCATA TATATATACA TATGCTAGTA - TCACGCGAGA TCGATAGTGA TCGCTGCGTA TCTGACGTCA TGAGTCAGTA - TGTAGTGTGA TGTCACACGA TGTCGTCGCA ACACATACGC ACAGTCGTGC - ACATGACGAC ACGACAGCTC ACGTCTCATC ACTCATCTAC ACTCGCGCAC - AGAGCGTCAC AGCGACTAGC AGTAGTGATC AGTGACACAC AGTGTATGTC - ATAGATAGAC ATATAGTCGC ATCTACTGAC CACGTAGATC CACGTGTCGC - CATACTCTAC CGACACTATC CGAGACGCGC CGTATGCGAC CGTCGATCTC - CTACGACTGC CTAGTCACTC CTCTACGCTC CTGTACATAC TAGACTGCAC - TAGCGCGCGC TAGCTCTATC TATAGACATC TATGATACGC TCACTCATAC - TCATCGAGTC TCGAGCTCTC TCGCAGACAC TCTGTCTCGC TGAGTGACGC - TGATGTGTAC TGCTATAGAC TGCTCGCTAC ACGTGCAGCG ACTCACAGAG - AGACTCAGCG AGAGAGTGTG AGCTATCGCG AGTCTGACTG AGTGAGCTCG - ATAGCTCTCG ATCACGTGCG ATCGTAGCAG ATCGTCTGTG ATGTACGATG - ATGTGTCTAG CACACGATAG CACTCGCACG CAGACGTCTG CAGTACTGCG - CGACAGCGAG CGATCTGTCG CGCGTGCTAG CGCTCGAGTG CGTGATGACG - CTATGTACAG CTCGATATAG CTCGCACGCG CTGCGTCACG CTGTGCGTCG - TAGCATACTG TATACATGTG TATCACTCAG TATCTGATAG TCGTGACATG - TCTGATCGAG TGACATCTCG TGAGCTAGAG TGATAGAGCG TGCGTGTGCG - TGCTAGTCAG TGTATCACAG TGTGCGCGTG ACACGACGAC ACACGTAGTA - ACACTACTCG ACGACACGTA ACGAGTAGAC ACGCGTCTAG ACGTACACAC - ACGTACTGTG ACGTAGATCG ACTACGTCTC ACTATACGAG ACTCGCGTCG -} - - -count_hash = Hash.new { |hash, key| hash[key] = 0 } -mid_hash = {} - -mids.each_with_index do |mid, i| - mid_hash[mid] = true -end - -casts = [] -casts << {:long=>'pos', :short=>'p', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil} - -options = Biopieces.options_parse(ARGV, casts) - -pos = options[:pos] - -Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| - input.each_record do |record| - if record.has_key? :SEQ - tag = record[:SEQ][pos ... pos + MID_LEN].upcase - - if mid_hash.has_key? tag - count_hash[tag] += 1 - end - end - output.puts record - end - - mids.each_with_index do |mid, i| - if count_hash[mid] > 0 - record = {} - record[:REC_TYPE] = "MID" - record[:MID_NUM] = i + 1 - record[:MID_COUNT] = count_hash[mid] - record[:MID_SEQ] = mid - output.puts record - end - end -end - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -__END__ diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa deleted file mode 100755 index f594d80..0000000 --- a/bp_bin/read_solexa +++ /dev/null @@ -1,106 +0,0 @@ -#!/usr/bin/env perl - -# Copyright (C) 2007-2009 Martin A. Hansen. - -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License -# as published by the Free Software Foundation; either version 2 -# of the License, or (at your option) any later version. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - -# http://www.gnu.org/copyleft/gpl.html - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - -# Read Solexa entries from one or more files. - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -use warnings; -use strict; -use Data::Dumper; -use Maasha::Biopieces; -use Maasha::Filesys; -use Maasha::Solexa; -use Maasha::Fastq; - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -my ( $options, $in, $out, $record, $data_in, $num, $entry, @seqs, @scores, $i ); - -$options = Maasha::Biopieces::parse_options( - [ - { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' }, - { long => 'convert2dec', short => 'c', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'cutoff', short => 'C', type => 'int', mandatory => 'no', default => 20, allowed => undef, disallowed => undef }, - { long => 'soft_mask', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - ] -); - -$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); -$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); - -while ( $record = Maasha::Biopieces::get_record( $in ) ) { - Maasha::Biopieces::put_record( $record, $out ); -} - -if ( $options->{ 'data_in' } ) -{ - $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } ); - - $num = 1; - - while ( $entry = Maasha::Fastq::get_entry( $data_in ) ) - { - if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) ) - { - Maasha::Fastq::softmask_solexa_str( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'cutoff' } ) if $options->{ 'soft_mask' }; - $record->{ 'SCORES' } = Maasha::Fastq::solexa_str2dec_str( $record->{ 'SCORES' } ) if $options->{ 'convert2dec' }; - - Maasha::Biopieces::put_record( $record, $out ); - } - - last if $options->{ "num" } and $num == $options->{ "num" }; - - $num++; - } - - close $data_in; -} - -Maasha::Biopieces::close_stream( $in ); -Maasha::Biopieces::close_stream( $out ); - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -BEGIN -{ - Maasha::Biopieces::status_set(); -} - - -END -{ - Maasha::Biopieces::status_log(); -} - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -__END__ diff --git a/bp_bin/remove_mids b/bp_bin/remove_mids deleted file mode 100755 index c73d23c..0000000 --- a/bp_bin/remove_mids +++ /dev/null @@ -1,310 +0,0 @@ -#!/usr/bin/env ruby - -# Copyright (C) 2007-2011 Martin A. Hansen. - -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License -# as published by the Free Software Foundation; either version 2 -# of the License, or (at your option) any later version. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - -# http://www.gnu.org/copyleft/gpl.html - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - -# This program is part of the Biopieces framework (www.biopieces.org). - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - -# Find MID tags in sequences in the stream. - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - -require 'maasha/biopieces' -require 'maasha/bits' -require 'pp' - -GS_SIZE = 10 -RL_SIZE = 11 - -GSMID_HASH = { - ACGAGTGCGT: "MID1", - TCTCTATGCG: "MID10", - TAGACTGCAC: "MID100", - TAGCGCGCGC: "MID101", - TAGCTCTATC: "MID102", - TATAGACATC: "MID103", - TATGATACGC: "MID104", - TCACTCATAC: "MID105", - TCATCGAGTC: "MID106", - TCGAGCTCTC: "MID107", - TCGCAGACAC: "MID108", - TCTGTCTCGC: "MID109", - TGATACGTCT: "MID11", - TGAGTGACGC: "MID110", - TGATGTGTAC: "MID111", - TGCTATAGAC: "MID112", - TGCTCGCTAC: "MID113", - ACGTGCAGCG: "MID114", - ACTCACAGAG: "MID115", - AGACTCAGCG: "MID116", - AGAGAGTGTG: "MID117", - AGCTATCGCG: "MID118", - AGTCTGACTG: "MID119", - TACTGAGCTA: "MID12", - AGTGAGCTCG: "MID120", - ATAGCTCTCG: "MID121", - ATCACGTGCG: "MID122", - ATCGTAGCAG: "MID123", - ATCGTCTGTG: "MID124", - ATGTACGATG: "MID125", - ATGTGTCTAG: "MID126", - CACACGATAG: "MID127", - CACTCGCACG: "MID128", - CAGACGTCTG: "MID129", - CATAGTAGTG: "MID13", - CAGTACTGCG: "MID130", - CGACAGCGAG: "MID131", - CGATCTGTCG: "MID132", - CGCGTGCTAG: "MID133", - CGCTCGAGTG: "MID134", - CGTGATGACG: "MID135", - CTATGTACAG: "MID136", - CTCGATATAG: "MID137", - CTCGCACGCG: "MID138", - CTGCGTCACG: "MID139", - CGAGAGATAC: "MID14", - CTGTGCGTCG: "MID140", - TAGCATACTG: "MID141", - TATACATGTG: "MID142", - TATCACTCAG: "MID143", - TATCTGATAG: "MID144", - TCGTGACATG: "MID145", - TCTGATCGAG: "MID146", - TGACATCTCG: "MID147", - TGAGCTAGAG: "MID148", - TGATAGAGCG: "MID149", - ATACGACGTA: "MID15", - TGCGTGTGCG: "MID150", - TGCTAGTCAG: "MID151", - TGTATCACAG: "MID152", - TGTGCGCGTG: "MID153", - TCACGTACTA: "MID16", - CGTCTAGTAC: "MID17", - TCTACGTAGC: "MID18", - TGTACTACTC: "MID19", - ACGCTCGACA: "MID2", - ACGACTACAG: "MID20", - CGTAGACTAG: "MID21", - TACGAGTATG: "MID22", - TACTCTCGTG: "MID23", - TAGAGACGAG: "MID24", - TCGTCGCTCG: "MID25", - ACATACGCGT: "MID26", - ACGCGAGTAT: "MID27", - ACTACTATGT: "MID28", - ACTGTACAGT: "MID29", - AGACGCACTC: "MID3", - AGACTATACT: "MID30", - AGCGTCGTCT: "MID31", - AGTACGCTAT: "MID32", - ATAGAGTACT: "MID33", - CACGCTACGT: "MID34", - CAGTAGACGT: "MID35", - CGACGTGACT: "MID36", - TACACACACT: "MID37", - TACACGTGAT: "MID38", - TACAGATCGT: "MID39", - AGCACTGTAG: "MID4", - TACGCTGTCT: "MID40", - TAGTGTAGAT: "MID41", - TCGATCACGT: "MID42", - TCGCACTAGT: "MID43", - TCTAGCGACT: "MID44", - TCTATACTAT: "MID45", - TGACGTATGT: "MID46", - TGTGAGTAGT: "MID47", - ACAGTATATA: "MID48", - ACGCGATCGA: "MID49", - ATCAGACACG: "MID5", - ACTAGCAGTA: "MID50", - AGCTCACGTA: "MID51", - AGTATACATA: "MID52", - AGTCGAGAGA: "MID53", - AGTGCTACGA: "MID54", - CGATCGTATA: "MID55", - CGCAGTACGA: "MID56", - CGCGTATACA: "MID57", - CGTACAGTCA: "MID58", - CGTACTCAGA: "MID59", - ATATCGCGAG: "MID6", - CTACGCTCTA: "MID60", - CTATAGCGTA: "MID61", - TACGTCATCA: "MID62", - TAGTCGCATA: "MID63", - TATATATACA: "MID64", - TATGCTAGTA: "MID65", - TCACGCGAGA: "MID66", - TCGATAGTGA: "MID67", - TCGCTGCGTA: "MID68", - TCTGACGTCA: "MID69", - CGTGTCTCTA: "MID7", - TGAGTCAGTA: "MID70", - TGTAGTGTGA: "MID71", - TGTCACACGA: "MID72", - TGTCGTCGCA: "MID73", - ACACATACGC: "MID74", - ACAGTCGTGC: "MID75", - ACATGACGAC: "MID76", - ACGACAGCTC: "MID77", - ACGTCTCATC: "MID78", - ACTCATCTAC: "MID79", - CTCGCGTGTC: "MID8", - ACTCGCGCAC: "MID80", - AGAGCGTCAC: "MID81", - AGCGACTAGC: "MID82", - AGTAGTGATC: "MID83", - AGTGACACAC: "MID84", - AGTGTATGTC: "MID85", - ATAGATAGAC: "MID86", - ATATAGTCGC: "MID87", - ATCTACTGAC: "MID88", - CACGTAGATC: "MID89", - TAGTATCAGC: "MID9", - CACGTGTCGC: "MID90", - CATACTCTAC: "MID91", - CGACACTATC: "MID92", - CGAGACGCGC: "MID93", - CGTATGCGAC: "MID94", - CGTCGATCTC: "MID95", - CTACGACTGC: "MID96", - CTAGTCACTC: "MID97", - CTCTACGCTC: "MID98", - CTGTACATAC: "MID99", -} - -RLMID_HASH = { - ACACGACGACT: "RL1", - ACACGTAGTAT: "RL2", - ACACTACTCGT: "RL3", - ACGACACGTAT: "RL4", - ACGAGTAGACT: "RL5", - ACGCGTCTAGT: "RL6", - ACGTACACACT: "RL7", - ACGTACTGTGT: "RL8", - ACGTAGATCGT: "RL9", - ACTACGTCTCT: "RL10", - ACTATACGAGT: "RL11", - ACTCGCGTCGT: "RL12" -} - -class MIDfinder - def initialize(mid_hash, pos, size, max_mismatches) - @mid_hash = mid_hash - @pos = pos - @size = size - @max_mismatches = max_mismatches - end - - def find_mid(seq) - hamming_dist = 0 - tag = seq[@pos ... @pos + @size].upcase.to_sym - - if @mid_hash.has_key? tag - return MID.new(tag, @mid_hash[tag], @pos, @size, hamming_dist) - elsif @max_mismatches > 0 - @mid_hash.each_pair do |mid, mid_name| - hamming_dist = tag.to_s.hamming_distance(mid.to_s) - - if hamming_dist <= @max_mismatches - return MID.new(mid, @mid_hash[mid], @pos, @size, hamming_dist) - end - end - end - - nil - end - - private - - # Class to hold a MID object. - class MID - attr_accessor :tag, :name, :pos, :len, :mismatches - - def initialize(tag, name, pos, len, mismatches) - @tag = tag - @name = name - @pos = pos - @len = len - @mismatches = mismatches - end - - def to_hash - hash = {} - hash[:MID] = @tag - hash[:MID_NAME] = @name - hash[:MID_POS] = @pos - hash[:MID_LEN] = @len - hash[:MID_MISMATCHES] = @mismatches - hash - end - - def start - @pos + @len - end - end -end -casts = [] -casts << {:long=>'pos', :short=>'p', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>nil, :disallowed=>nil} -casts << {:long=>'mismatches', :short=>'m', :type=>'uint', :mandatory=>false, :default=>0, :allowed=>"0,1,2", :disallowed=>nil} -casts << {:long=>'gsmids', :short=>'g', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} -casts << {:long=>'rlmids', :short=>'r', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil} - -options = Biopieces.options_parse(ARGV, casts) - -raise "Can't remove only GSMIDs and only RLMIDs simultaniously." if options[:rlmids] and options[:gsmids] - -pos = options[:pos] -mismatches = options[:mismatches] - -gsfinder = MIDfinder.new(GSMID_HASH, options[:pos], GS_SIZE, options[:mismatches]) -rlfinder = MIDfinder.new(RLMID_HASH, options[:pos], RL_SIZE, options[:mismatches]) - -Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output| - input.each_record do |record| - if record.has_key? :SEQ - - if options[:gsmids] - mid = gsfinder.find_mid(record[:SEQ]) - elsif options[:rlmids] - mid = rlfinder.find_mid(record[:SEQ]) - else - mid = gsfinder.find_mid(record[:SEQ]) || rlfinder.find_mid(record[:SEQ]) - end - - if mid - record.merge!(mid.to_hash) - - record[:SEQ] = record[:SEQ][mid.start .. -1] - record[:SCORES] = record[:SCORES][mid.start .. -1] if record[:SCORES] - record[:SEQ_LEN] = record[:SEQ].length - end - end - - output.puts record - end -end - - -# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< - - -__END__ diff --git a/bp_test/in/find_mids.in.1 b/bp_test/in/find_mids.in.1 deleted file mode 100644 index 8dd5ce5..0000000 --- a/bp_test/in/find_mids.in.1 +++ /dev/null @@ -1,306 +0,0 @@ -SEQ: atcgACGAGTGCGTatcg ---- -SEQ: atcgACGCTCGACAatcg ---- -SEQ: atcgAGACGCACTCatcg ---- -SEQ: atcgAGCACTGTAGatcg ---- -SEQ: atcgATCAGACACGatcg ---- -SEQ: atcgATATCGCGAGatcg ---- -SEQ: atcgCGTGTCTCTAatcg ---- -SEQ: atcgCTCGCGTGTCatcg ---- -SEQ: atcgTAGTATCAGCatcg ---- -SEQ: atcgTCTCTATGCGatcg ---- -SEQ: atcgTGATACGTCTatcg ---- -SEQ: atcgTACTGAGCTAatcg ---- -SEQ: atcgCATAGTAGTGatcg ---- -SEQ: atcgCGAGAGATACatcg ---- -SEQ: atcgATACGACGTAatcg ---- -SEQ: atcgTCACGTACTAatcg ---- -SEQ: atcgCGTCTAGTACatcg ---- -SEQ: atcgTCTACGTAGCatcg ---- -SEQ: atcgTGTACTACTCatcg ---- -SEQ: atcgACGACTACAGatcg ---- -SEQ: atcgCGTAGACTAGatcg ---- -SEQ: atcgTACGAGTATGatcg ---- -SEQ: atcgTACTCTCGTGatcg ---- -SEQ: atcgTAGAGACGAGatcg ---- -SEQ: atcgTCGTCGCTCGatcg ---- -SEQ: atcgACATACGCGTatcg ---- -SEQ: atcgACGCGAGTATatcg ---- -SEQ: atcgACTACTATGTatcg ---- -SEQ: atcgACTGTACAGTatcg ---- -SEQ: atcgAGACTATACTatcg ---- -SEQ: atcgAGCGTCGTCTatcg ---- -SEQ: atcgAGTACGCTATatcg ---- -SEQ: atcgATAGAGTACTatcg ---- -SEQ: atcgCACGCTACGTatcg ---- -SEQ: atcgCAGTAGACGTatcg ---- -SEQ: atcgCGACGTGACTatcg ---- -SEQ: atcgTACACACACTatcg ---- -SEQ: atcgTACACGTGATatcg ---- -SEQ: atcgTACAGATCGTatcg ---- -SEQ: atcgTACGCTGTCTatcg ---- -SEQ: atcgTAGTGTAGATatcg ---- -SEQ: atcgTCGATCACGTatcg ---- -SEQ: atcgTCGCACTAGTatcg ---- -SEQ: atcgTCTAGCGACTatcg ---- -SEQ: atcgTCTATACTATatcg ---- -SEQ: atcgTGACGTATGTatcg ---- -SEQ: atcgTGTGAGTAGTatcg ---- -SEQ: atcgACAGTATATAatcg ---- -SEQ: atcgACGCGATCGAatcg ---- -SEQ: atcgACTAGCAGTAatcg ---- -SEQ: atcgAGCTCACGTAatcg ---- -SEQ: atcgAGTATACATAatcg ---- -SEQ: atcgAGTCGAGAGAatcg ---- -SEQ: atcgAGTGCTACGAatcg ---- -SEQ: atcgCGATCGTATAatcg ---- -SEQ: atcgCGCAGTACGAatcg ---- -SEQ: atcgCGCGTATACAatcg ---- -SEQ: atcgCGTACAGTCAatcg ---- -SEQ: atcgCGTACTCAGAatcg ---- -SEQ: atcgCTACGCTCTAatcg ---- -SEQ: atcgCTATAGCGTAatcg ---- -SEQ: atcgTACGTCATCAatcg ---- -SEQ: atcgTAGTCGCATAatcg ---- -SEQ: atcgTATATATACAatcg ---- -SEQ: atcgTATGCTAGTAatcg ---- -SEQ: atcgTCACGCGAGAatcg ---- -SEQ: atcgTCGATAGTGAatcg ---- -SEQ: atcgTCGCTGCGTAatcg ---- -SEQ: atcgTCTGACGTCAatcg ---- -SEQ: atcgTGAGTCAGTAatcg ---- -SEQ: atcgTGTAGTGTGAatcg ---- -SEQ: atcgTGTCACACGAatcg ---- -SEQ: atcgTGTCGTCGCAatcg ---- -SEQ: atcgACACATACGCatcg ---- -SEQ: atcgACAGTCGTGCatcg ---- -SEQ: atcgACATGACGACatcg ---- -SEQ: atcgACGACAGCTCatcg ---- -SEQ: atcgACGTCTCATCatcg ---- -SEQ: atcgACTCATCTACatcg ---- -SEQ: atcgACTCGCGCACatcg ---- -SEQ: atcgAGAGCGTCACatcg ---- -SEQ: atcgAGCGACTAGCatcg ---- -SEQ: atcgAGTAGTGATCatcg ---- -SEQ: atcgAGTGACACACatcg ---- -SEQ: atcgAGTGTATGTCatcg ---- -SEQ: atcgATAGATAGACatcg ---- -SEQ: atcgATATAGTCGCatcg ---- -SEQ: atcgATCTACTGACatcg ---- -SEQ: atcgCACGTAGATCatcg ---- -SEQ: atcgCACGTGTCGCatcg ---- -SEQ: atcgCATACTCTACatcg ---- -SEQ: atcgCGACACTATCatcg ---- -SEQ: atcgCGAGACGCGCatcg ---- -SEQ: atcgCGTATGCGACatcg ---- -SEQ: atcgCGTCGATCTCatcg ---- -SEQ: atcgCTACGACTGCatcg ---- -SEQ: atcgCTAGTCACTCatcg ---- -SEQ: atcgCTCTACGCTCatcg ---- -SEQ: atcgCTGTACATACatcg ---- -SEQ: atcgTAGACTGCACatcg ---- -SEQ: atcgTAGCGCGCGCatcg ---- -SEQ: atcgTAGCTCTATCatcg ---- -SEQ: atcgTATAGACATCatcg ---- -SEQ: atcgTATGATACGCatcg ---- -SEQ: atcgTCACTCATACatcg ---- -SEQ: atcgTCATCGAGTCatcg ---- -SEQ: atcgTCGAGCTCTCatcg ---- -SEQ: atcgTCGCAGACACatcg ---- -SEQ: atcgTCTGTCTCGCatcg ---- -SEQ: atcgTGAGTGACGCatcg ---- -SEQ: atcgTGATGTGTACatcg ---- -SEQ: atcgTGCTATAGACatcg ---- -SEQ: atcgTGCTCGCTACatcg ---- -SEQ: atcgACGTGCAGCGatcg ---- -SEQ: atcgACTCACAGAGatcg ---- -SEQ: atcgAGACTCAGCGatcg ---- -SEQ: atcgAGAGAGTGTGatcg ---- -SEQ: atcgAGCTATCGCGatcg ---- -SEQ: atcgAGTCTGACTGatcg ---- -SEQ: atcgAGTGAGCTCGatcg ---- -SEQ: atcgATAGCTCTCGatcg ---- -SEQ: atcgATCACGTGCGatcg ---- -SEQ: atcgATCGTAGCAGatcg ---- -SEQ: atcgATCGTCTGTGatcg ---- -SEQ: atcgATGTACGATGatcg ---- -SEQ: atcgATGTGTCTAGatcg ---- -SEQ: atcgCACACGATAGatcg ---- -SEQ: atcgCACTCGCACGatcg ---- -SEQ: atcgCAGACGTCTGatcg ---- -SEQ: atcgCAGTACTGCGatcg ---- -SEQ: atcgCGACAGCGAGatcg ---- -SEQ: atcgCGATCTGTCGatcg ---- -SEQ: atcgCGCGTGCTAGatcg ---- -SEQ: atcgCGCTCGAGTGatcg ---- -SEQ: atcgCGTGATGACGatcg ---- -SEQ: atcgCTATGTACAGatcg ---- -SEQ: atcgCTCGATATAGatcg ---- -SEQ: atcgCTCGCACGCGatcg ---- -SEQ: atcgCTGCGTCACGatcg ---- -SEQ: atcgCTGTGCGTCGatcg ---- -SEQ: atcgTAGCATACTGatcg ---- -SEQ: atcgTATACATGTGatcg ---- -SEQ: atcgTATCACTCAGatcg ---- -SEQ: atcgTATCTGATAGatcg ---- -SEQ: atcgTCGTGACATGatcg ---- -SEQ: atcgTCTGATCGAGatcg ---- -SEQ: atcgTGACATCTCGatcg ---- -SEQ: atcgTGAGCTAGAGatcg ---- -SEQ: atcgTGATAGAGCGatcg ---- -SEQ: atcgTGCGTGTGCGatcg ---- -SEQ: atcgTGCTAGTCAGatcg ---- -SEQ: atcgTGTATCACAGatcg ---- -SEQ: atcgTGTGCGCGTGatcg ---- diff --git a/bp_test/in/find_mids.in.2 b/bp_test/in/find_mids.in.2 deleted file mode 100644 index 2441241..0000000 --- a/bp_test/in/find_mids.in.2 +++ /dev/null @@ -1,306 +0,0 @@ -SEQ: ACGAGTGCGTatcg ---- -SEQ: ACGCTCGACAatcg ---- -SEQ: AGACGCACTCatcg ---- -SEQ: AGCACTGTAGatcg ---- -SEQ: ATCAGACACGatcg ---- -SEQ: ATATCGCGAGatcg ---- -SEQ: CGTGTCTCTAatcg ---- -SEQ: CTCGCGTGTCatcg ---- -SEQ: TAGTATCAGCatcg ---- -SEQ: TCTCTATGCGatcg ---- -SEQ: TGATACGTCTatcg ---- -SEQ: TACTGAGCTAatcg ---- -SEQ: CATAGTAGTGatcg ---- -SEQ: CGAGAGATACatcg ---- -SEQ: ATACGACGTAatcg ---- -SEQ: TCACGTACTAatcg ---- -SEQ: CGTCTAGTACatcg ---- -SEQ: TCTACGTAGCatcg ---- -SEQ: TGTACTACTCatcg ---- -SEQ: ACGACTACAGatcg ---- -SEQ: CGTAGACTAGatcg ---- -SEQ: TACGAGTATGatcg ---- -SEQ: TACTCTCGTGatcg ---- -SEQ: TAGAGACGAGatcg ---- -SEQ: TCGTCGCTCGatcg ---- -SEQ: ACATACGCGTatcg ---- -SEQ: ACGCGAGTATatcg ---- -SEQ: ACTACTATGTatcg ---- -SEQ: ACTGTACAGTatcg ---- -SEQ: AGACTATACTatcg ---- -SEQ: AGCGTCGTCTatcg ---- -SEQ: AGTACGCTATatcg ---- -SEQ: ATAGAGTACTatcg ---- -SEQ: CACGCTACGTatcg ---- -SEQ: CAGTAGACGTatcg ---- -SEQ: CGACGTGACTatcg ---- -SEQ: TACACACACTatcg ---- -SEQ: TACACGTGATatcg ---- -SEQ: TACAGATCGTatcg ---- -SEQ: TACGCTGTCTatcg ---- -SEQ: TAGTGTAGATatcg ---- -SEQ: TCGATCACGTatcg ---- -SEQ: TCGCACTAGTatcg ---- -SEQ: TCTAGCGACTatcg ---- -SEQ: TCTATACTATatcg ---- -SEQ: TGACGTATGTatcg ---- -SEQ: TGTGAGTAGTatcg ---- -SEQ: ACAGTATATAatcg ---- -SEQ: ACGCGATCGAatcg ---- -SEQ: ACTAGCAGTAatcg ---- -SEQ: AGCTCACGTAatcg ---- -SEQ: AGTATACATAatcg ---- -SEQ: AGTCGAGAGAatcg ---- -SEQ: AGTGCTACGAatcg ---- -SEQ: CGATCGTATAatcg ---- -SEQ: CGCAGTACGAatcg ---- -SEQ: CGCGTATACAatcg ---- -SEQ: CGTACAGTCAatcg ---- -SEQ: CGTACTCAGAatcg ---- -SEQ: CTACGCTCTAatcg ---- -SEQ: CTATAGCGTAatcg ---- -SEQ: TACGTCATCAatcg ---- -SEQ: TAGTCGCATAatcg ---- -SEQ: TATATATACAatcg ---- -SEQ: TATGCTAGTAatcg ---- -SEQ: TCACGCGAGAatcg ---- -SEQ: TCGATAGTGAatcg ---- -SEQ: TCGCTGCGTAatcg ---- -SEQ: TCTGACGTCAatcg ---- -SEQ: TGAGTCAGTAatcg ---- -SEQ: TGTAGTGTGAatcg ---- -SEQ: TGTCACACGAatcg ---- -SEQ: TGTCGTCGCAatcg ---- -SEQ: ACACATACGCatcg ---- -SEQ: ACAGTCGTGCatcg ---- -SEQ: ACATGACGACatcg ---- -SEQ: ACGACAGCTCatcg ---- -SEQ: ACGTCTCATCatcg ---- -SEQ: ACTCATCTACatcg ---- -SEQ: ACTCGCGCACatcg ---- -SEQ: AGAGCGTCACatcg ---- -SEQ: AGCGACTAGCatcg ---- -SEQ: AGTAGTGATCatcg ---- -SEQ: AGTGACACACatcg ---- -SEQ: AGTGTATGTCatcg ---- -SEQ: ATAGATAGACatcg ---- -SEQ: ATATAGTCGCatcg ---- -SEQ: ATCTACTGACatcg ---- -SEQ: CACGTAGATCatcg ---- -SEQ: CACGTGTCGCatcg ---- -SEQ: CATACTCTACatcg ---- -SEQ: CGACACTATCatcg ---- -SEQ: CGAGACGCGCatcg ---- -SEQ: CGTATGCGACatcg ---- -SEQ: CGTCGATCTCatcg ---- -SEQ: CTACGACTGCatcg ---- -SEQ: CTAGTCACTCatcg ---- -SEQ: CTCTACGCTCatcg ---- -SEQ: CTGTACATACatcg ---- -SEQ: TAGACTGCACatcg ---- -SEQ: TAGCGCGCGCatcg ---- -SEQ: TAGCTCTATCatcg ---- -SEQ: TATAGACATCatcg ---- -SEQ: TATGATACGCatcg ---- -SEQ: TCACTCATACatcg ---- -SEQ: TCATCGAGTCatcg ---- -SEQ: TCGAGCTCTCatcg ---- -SEQ: TCGCAGACACatcg ---- -SEQ: TCTGTCTCGCatcg ---- -SEQ: TGAGTGACGCatcg ---- -SEQ: TGATGTGTACatcg ---- -SEQ: TGCTATAGACatcg ---- -SEQ: TGCTCGCTACatcg ---- -SEQ: ACGTGCAGCGatcg ---- -SEQ: ACTCACAGAGatcg ---- -SEQ: AGACTCAGCGatcg ---- -SEQ: AGAGAGTGTGatcg ---- -SEQ: AGCTATCGCGatcg ---- -SEQ: AGTCTGACTGatcg ---- -SEQ: AGTGAGCTCGatcg ---- -SEQ: ATAGCTCTCGatcg ---- -SEQ: ATCACGTGCGatcg ---- -SEQ: ATCGTAGCAGatcg ---- -SEQ: ATCGTCTGTGatcg ---- -SEQ: ATGTACGATGatcg ---- -SEQ: ATGTGTCTAGatcg ---- -SEQ: CACACGATAGatcg ---- -SEQ: CACTCGCACGatcg ---- -SEQ: CAGACGTCTGatcg ---- -SEQ: CAGTACTGCGatcg ---- -SEQ: CGACAGCGAGatcg ---- -SEQ: CGATCTGTCGatcg ---- -SEQ: CGCGTGCTAGatcg ---- -SEQ: CGCTCGAGTGatcg ---- -SEQ: CGTGATGACGatcg ---- -SEQ: CTATGTACAGatcg ---- -SEQ: CTCGATATAGatcg ---- -SEQ: CTCGCACGCGatcg ---- -SEQ: CTGCGTCACGatcg ---- -SEQ: CTGTGCGTCGatcg ---- -SEQ: TAGCATACTGatcg ---- -SEQ: TATACATGTGatcg ---- -SEQ: TATCACTCAGatcg ---- -SEQ: TATCTGATAGatcg ---- -SEQ: TCGTGACATGatcg ---- -SEQ: TCTGATCGAGatcg ---- -SEQ: TGACATCTCGatcg ---- -SEQ: TGAGCTAGAGatcg ---- -SEQ: TGATAGAGCGatcg ---- -SEQ: TGCGTGTGCGatcg ---- -SEQ: TGCTAGTCAGatcg ---- -SEQ: TGTATCACAGatcg ---- -SEQ: TGTGCGCGTGatcg ---- diff --git a/bp_test/in/read_solexa.in b/bp_test/in/read_solexa.in deleted file mode 100644 index 9aff44f..0000000 --- a/bp_test/in/read_solexa.in +++ /dev/null @@ -1,12 +0,0 @@ -@HWI-EAS157_20FFGAAXX:2:1:888:434 -TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG -+HWI-EAS157_20FFGAAXX:2:1:888:434 -hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe -@HWI-EAS157_20FFGAAXX:2:1:898:373 -TTCTTGTTGTTGAAATACAACGATGGTTTTTCATAT -+HWI-EAS157_20FFGAAXX:2:1:898:373 -hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh -@HWI-EAS157_20FFGAAXX:2:1:907:487 -TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT -+HWI-EAS157_20FFGAAXX:2:1:907:487 -hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh diff --git a/bp_test/in/remove_mids.in b/bp_test/in/remove_mids.in deleted file mode 100644 index c8e8716..0000000 --- a/bp_test/in/remove_mids.in +++ /dev/null @@ -1,32 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: atcgACTCGCGTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: atcgACTCGCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: atcgCTGTACATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: atcgCTGTtCATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- diff --git a/bp_test/out/find_mids.out.1 b/bp_test/out/find_mids.out.1 deleted file mode 100644 index 6454c3e..0000000 --- a/bp_test/out/find_mids.out.1 +++ /dev/null @@ -1,1071 +0,0 @@ -SEQ: atcgACGAGTGCGTatcg ---- -SEQ: atcgACGCTCGACAatcg ---- -SEQ: atcgAGACGCACTCatcg ---- -SEQ: atcgAGCACTGTAGatcg ---- -SEQ: atcgATCAGACACGatcg ---- -SEQ: atcgATATCGCGAGatcg ---- -SEQ: atcgCGTGTCTCTAatcg ---- -SEQ: atcgCTCGCGTGTCatcg ---- -SEQ: atcgTAGTATCAGCatcg ---- -SEQ: atcgTCTCTATGCGatcg ---- -SEQ: atcgTGATACGTCTatcg ---- -SEQ: atcgTACTGAGCTAatcg ---- -SEQ: atcgCATAGTAGTGatcg ---- -SEQ: atcgCGAGAGATACatcg ---- -SEQ: atcgATACGACGTAatcg ---- -SEQ: atcgTCACGTACTAatcg ---- -SEQ: atcgCGTCTAGTACatcg ---- -SEQ: atcgTCTACGTAGCatcg ---- -SEQ: atcgTGTACTACTCatcg ---- -SEQ: atcgACGACTACAGatcg ---- -SEQ: atcgCGTAGACTAGatcg ---- -SEQ: atcgTACGAGTATGatcg ---- -SEQ: atcgTACTCTCGTGatcg ---- -SEQ: atcgTAGAGACGAGatcg ---- -SEQ: atcgTCGTCGCTCGatcg ---- -SEQ: atcgACATACGCGTatcg ---- -SEQ: atcgACGCGAGTATatcg ---- -SEQ: atcgACTACTATGTatcg ---- -SEQ: atcgACTGTACAGTatcg ---- -SEQ: atcgAGACTATACTatcg ---- -SEQ: atcgAGCGTCGTCTatcg ---- -SEQ: atcgAGTACGCTATatcg ---- -SEQ: atcgATAGAGTACTatcg ---- -SEQ: atcgCACGCTACGTatcg ---- -SEQ: atcgCAGTAGACGTatcg ---- -SEQ: atcgCGACGTGACTatcg ---- -SEQ: atcgTACACACACTatcg ---- -SEQ: atcgTACACGTGATatcg ---- -SEQ: atcgTACAGATCGTatcg ---- -SEQ: atcgTACGCTGTCTatcg ---- -SEQ: atcgTAGTGTAGATatcg ---- -SEQ: atcgTCGATCACGTatcg ---- -SEQ: atcgTCGCACTAGTatcg ---- -SEQ: atcgTCTAGCGACTatcg ---- -SEQ: atcgTCTATACTATatcg ---- -SEQ: atcgTGACGTATGTatcg ---- -SEQ: atcgTGTGAGTAGTatcg ---- -SEQ: atcgACAGTATATAatcg ---- -SEQ: atcgACGCGATCGAatcg ---- -SEQ: atcgACTAGCAGTAatcg ---- -SEQ: atcgAGCTCACGTAatcg ---- -SEQ: atcgAGTATACATAatcg ---- -SEQ: atcgAGTCGAGAGAatcg ---- -SEQ: atcgAGTGCTACGAatcg ---- -SEQ: atcgCGATCGTATAatcg ---- -SEQ: atcgCGCAGTACGAatcg ---- -SEQ: atcgCGCGTATACAatcg ---- -SEQ: atcgCGTACAGTCAatcg ---- -SEQ: atcgCGTACTCAGAatcg ---- -SEQ: atcgCTACGCTCTAatcg ---- -SEQ: atcgCTATAGCGTAatcg ---- -SEQ: atcgTACGTCATCAatcg ---- -SEQ: atcgTAGTCGCATAatcg ---- -SEQ: atcgTATATATACAatcg ---- -SEQ: atcgTATGCTAGTAatcg ---- -SEQ: atcgTCACGCGAGAatcg ---- -SEQ: atcgTCGATAGTGAatcg ---- -SEQ: atcgTCGCTGCGTAatcg ---- -SEQ: atcgTCTGACGTCAatcg ---- -SEQ: atcgTGAGTCAGTAatcg ---- -SEQ: atcgTGTAGTGTGAatcg ---- -SEQ: atcgTGTCACACGAatcg ---- -SEQ: atcgTGTCGTCGCAatcg ---- -SEQ: atcgACACATACGCatcg ---- -SEQ: atcgACAGTCGTGCatcg ---- -SEQ: atcgACATGACGACatcg ---- -SEQ: atcgACGACAGCTCatcg ---- -SEQ: atcgACGTCTCATCatcg ---- -SEQ: atcgACTCATCTACatcg ---- -SEQ: atcgACTCGCGCACatcg ---- -SEQ: atcgAGAGCGTCACatcg ---- -SEQ: atcgAGCGACTAGCatcg ---- -SEQ: atcgAGTAGTGATCatcg ---- -SEQ: atcgAGTGACACACatcg ---- -SEQ: atcgAGTGTATGTCatcg ---- -SEQ: atcgATAGATAGACatcg ---- -SEQ: atcgATATAGTCGCatcg ---- -SEQ: atcgATCTACTGACatcg ---- -SEQ: atcgCACGTAGATCatcg ---- -SEQ: atcgCACGTGTCGCatcg ---- -SEQ: atcgCATACTCTACatcg ---- -SEQ: atcgCGACACTATCatcg ---- -SEQ: atcgCGAGACGCGCatcg ---- -SEQ: atcgCGTATGCGACatcg ---- -SEQ: atcgCGTCGATCTCatcg ---- -SEQ: atcgCTACGACTGCatcg ---- -SEQ: atcgCTAGTCACTCatcg ---- -SEQ: atcgCTCTACGCTCatcg ---- -SEQ: atcgCTGTACATACatcg ---- -SEQ: atcgTAGACTGCACatcg ---- -SEQ: atcgTAGCGCGCGCatcg ---- -SEQ: atcgTAGCTCTATCatcg ---- -SEQ: atcgTATAGACATCatcg ---- -SEQ: atcgTATGATACGCatcg ---- -SEQ: atcgTCACTCATACatcg ---- -SEQ: atcgTCATCGAGTCatcg ---- -SEQ: atcgTCGAGCTCTCatcg ---- -SEQ: atcgTCGCAGACACatcg ---- -SEQ: atcgTCTGTCTCGCatcg ---- -SEQ: atcgTGAGTGACGCatcg ---- -SEQ: atcgTGATGTGTACatcg ---- -SEQ: atcgTGCTATAGACatcg ---- -SEQ: atcgTGCTCGCTACatcg ---- -SEQ: atcgACGTGCAGCGatcg ---- -SEQ: atcgACTCACAGAGatcg ---- -SEQ: atcgAGACTCAGCGatcg ---- -SEQ: atcgAGAGAGTGTGatcg ---- -SEQ: atcgAGCTATCGCGatcg ---- -SEQ: atcgAGTCTGACTGatcg ---- -SEQ: atcgAGTGAGCTCGatcg ---- -SEQ: atcgATAGCTCTCGatcg ---- -SEQ: atcgATCACGTGCGatcg ---- -SEQ: atcgATCGTAGCAGatcg ---- -SEQ: atcgATCGTCTGTGatcg ---- -SEQ: atcgATGTACGATGatcg ---- -SEQ: atcgATGTGTCTAGatcg ---- -SEQ: atcgCACACGATAGatcg ---- -SEQ: atcgCACTCGCACGatcg ---- -SEQ: atcgCAGACGTCTGatcg ---- -SEQ: atcgCAGTACTGCGatcg ---- -SEQ: atcgCGACAGCGAGatcg ---- -SEQ: atcgCGATCTGTCGatcg ---- -SEQ: atcgCGCGTGCTAGatcg ---- -SEQ: atcgCGCTCGAGTGatcg ---- -SEQ: atcgCGTGATGACGatcg ---- -SEQ: atcgCTATGTACAGatcg ---- -SEQ: atcgCTCGATATAGatcg ---- -SEQ: atcgCTCGCACGCGatcg ---- -SEQ: atcgCTGCGTCACGatcg ---- -SEQ: atcgCTGTGCGTCGatcg ---- -SEQ: atcgTAGCATACTGatcg ---- -SEQ: atcgTATACATGTGatcg ---- -SEQ: atcgTATCACTCAGatcg ---- -SEQ: atcgTATCTGATAGatcg ---- -SEQ: atcgTCGTGACATGatcg ---- -SEQ: atcgTCTGATCGAGatcg ---- -SEQ: atcgTGACATCTCGatcg ---- -SEQ: atcgTGAGCTAGAGatcg ---- -SEQ: atcgTGATAGAGCGatcg ---- -SEQ: atcgTGCGTGTGCGatcg ---- -SEQ: atcgTGCTAGTCAGatcg ---- -SEQ: atcgTGTATCACAGatcg ---- -SEQ: atcgTGTGCGCGTGatcg ---- -REC_TYPE: MID -MID_NUM: 1 -MID_COUNT: 1 -MID_SEQ: ACGAGTGCGT ---- -REC_TYPE: MID -MID_NUM: 2 -MID_COUNT: 1 -MID_SEQ: ACGCTCGACA ---- -REC_TYPE: MID -MID_NUM: 3 -MID_COUNT: 1 -MID_SEQ: AGACGCACTC ---- -REC_TYPE: MID -MID_NUM: 4 -MID_COUNT: 1 -MID_SEQ: AGCACTGTAG ---- -REC_TYPE: MID -MID_NUM: 5 -MID_COUNT: 1 -MID_SEQ: ATCAGACACG ---- -REC_TYPE: MID -MID_NUM: 6 -MID_COUNT: 1 -MID_SEQ: ATATCGCGAG ---- -REC_TYPE: MID -MID_NUM: 7 -MID_COUNT: 1 -MID_SEQ: CGTGTCTCTA ---- -REC_TYPE: MID -MID_NUM: 8 -MID_COUNT: 1 -MID_SEQ: CTCGCGTGTC ---- -REC_TYPE: MID -MID_NUM: 9 -MID_COUNT: 1 -MID_SEQ: TAGTATCAGC ---- -REC_TYPE: MID -MID_NUM: 10 -MID_COUNT: 1 -MID_SEQ: TCTCTATGCG ---- -REC_TYPE: MID -MID_NUM: 11 -MID_COUNT: 1 -MID_SEQ: TGATACGTCT ---- -REC_TYPE: MID -MID_NUM: 12 -MID_COUNT: 1 -MID_SEQ: TACTGAGCTA ---- -REC_TYPE: MID -MID_NUM: 13 -MID_COUNT: 1 -MID_SEQ: CATAGTAGTG ---- -REC_TYPE: MID -MID_NUM: 14 -MID_COUNT: 1 -MID_SEQ: CGAGAGATAC ---- -REC_TYPE: MID -MID_NUM: 15 -MID_COUNT: 1 -MID_SEQ: ATACGACGTA ---- -REC_TYPE: MID -MID_NUM: 16 -MID_COUNT: 1 -MID_SEQ: TCACGTACTA ---- -REC_TYPE: MID -MID_NUM: 17 -MID_COUNT: 1 -MID_SEQ: CGTCTAGTAC ---- -REC_TYPE: MID -MID_NUM: 18 -MID_COUNT: 1 -MID_SEQ: TCTACGTAGC ---- -REC_TYPE: MID -MID_NUM: 19 -MID_COUNT: 1 -MID_SEQ: TGTACTACTC ---- -REC_TYPE: MID -MID_NUM: 20 -MID_COUNT: 1 -MID_SEQ: ACGACTACAG ---- -REC_TYPE: MID -MID_NUM: 21 -MID_COUNT: 1 -MID_SEQ: CGTAGACTAG ---- -REC_TYPE: MID -MID_NUM: 22 -MID_COUNT: 1 -MID_SEQ: TACGAGTATG ---- -REC_TYPE: MID -MID_NUM: 23 -MID_COUNT: 1 -MID_SEQ: TACTCTCGTG ---- -REC_TYPE: MID -MID_NUM: 24 -MID_COUNT: 1 -MID_SEQ: TAGAGACGAG ---- -REC_TYPE: MID -MID_NUM: 25 -MID_COUNT: 1 -MID_SEQ: TCGTCGCTCG ---- -REC_TYPE: MID -MID_NUM: 26 -MID_COUNT: 1 -MID_SEQ: ACATACGCGT ---- -REC_TYPE: MID -MID_NUM: 27 -MID_COUNT: 1 -MID_SEQ: ACGCGAGTAT ---- -REC_TYPE: MID -MID_NUM: 28 -MID_COUNT: 1 -MID_SEQ: ACTACTATGT ---- -REC_TYPE: MID -MID_NUM: 29 -MID_COUNT: 1 -MID_SEQ: ACTGTACAGT ---- -REC_TYPE: MID -MID_NUM: 30 -MID_COUNT: 1 -MID_SEQ: AGACTATACT ---- -REC_TYPE: MID -MID_NUM: 31 -MID_COUNT: 1 -MID_SEQ: AGCGTCGTCT ---- -REC_TYPE: MID -MID_NUM: 32 -MID_COUNT: 1 -MID_SEQ: AGTACGCTAT ---- -REC_TYPE: MID -MID_NUM: 33 -MID_COUNT: 1 -MID_SEQ: ATAGAGTACT ---- -REC_TYPE: MID -MID_NUM: 34 -MID_COUNT: 1 -MID_SEQ: CACGCTACGT ---- -REC_TYPE: MID -MID_NUM: 35 -MID_COUNT: 1 -MID_SEQ: CAGTAGACGT ---- -REC_TYPE: MID -MID_NUM: 36 -MID_COUNT: 1 -MID_SEQ: CGACGTGACT ---- -REC_TYPE: MID -MID_NUM: 37 -MID_COUNT: 1 -MID_SEQ: TACACACACT ---- -REC_TYPE: MID -MID_NUM: 38 -MID_COUNT: 1 -MID_SEQ: TACACGTGAT ---- -REC_TYPE: MID -MID_NUM: 39 -MID_COUNT: 1 -MID_SEQ: TACAGATCGT ---- -REC_TYPE: MID -MID_NUM: 40 -MID_COUNT: 1 -MID_SEQ: TACGCTGTCT ---- -REC_TYPE: MID -MID_NUM: 41 -MID_COUNT: 1 -MID_SEQ: TAGTGTAGAT ---- -REC_TYPE: MID -MID_NUM: 42 -MID_COUNT: 1 -MID_SEQ: TCGATCACGT ---- -REC_TYPE: MID -MID_NUM: 43 -MID_COUNT: 1 -MID_SEQ: TCGCACTAGT ---- -REC_TYPE: MID -MID_NUM: 44 -MID_COUNT: 1 -MID_SEQ: TCTAGCGACT ---- -REC_TYPE: MID -MID_NUM: 45 -MID_COUNT: 1 -MID_SEQ: TCTATACTAT ---- -REC_TYPE: MID -MID_NUM: 46 -MID_COUNT: 1 -MID_SEQ: TGACGTATGT ---- -REC_TYPE: MID -MID_NUM: 47 -MID_COUNT: 1 -MID_SEQ: TGTGAGTAGT ---- -REC_TYPE: MID -MID_NUM: 48 -MID_COUNT: 1 -MID_SEQ: ACAGTATATA ---- -REC_TYPE: MID -MID_NUM: 49 -MID_COUNT: 1 -MID_SEQ: ACGCGATCGA ---- -REC_TYPE: MID -MID_NUM: 50 -MID_COUNT: 1 -MID_SEQ: ACTAGCAGTA ---- -REC_TYPE: MID -MID_NUM: 51 -MID_COUNT: 1 -MID_SEQ: AGCTCACGTA ---- -REC_TYPE: MID -MID_NUM: 52 -MID_COUNT: 1 -MID_SEQ: AGTATACATA ---- -REC_TYPE: MID -MID_NUM: 53 -MID_COUNT: 1 -MID_SEQ: AGTCGAGAGA ---- -REC_TYPE: MID -MID_NUM: 54 -MID_COUNT: 1 -MID_SEQ: AGTGCTACGA ---- -REC_TYPE: MID -MID_NUM: 55 -MID_COUNT: 1 -MID_SEQ: CGATCGTATA ---- -REC_TYPE: MID -MID_NUM: 56 -MID_COUNT: 1 -MID_SEQ: CGCAGTACGA ---- -REC_TYPE: MID -MID_NUM: 57 -MID_COUNT: 1 -MID_SEQ: CGCGTATACA ---- -REC_TYPE: MID -MID_NUM: 58 -MID_COUNT: 1 -MID_SEQ: CGTACAGTCA ---- -REC_TYPE: MID -MID_NUM: 59 -MID_COUNT: 1 -MID_SEQ: CGTACTCAGA ---- -REC_TYPE: MID -MID_NUM: 60 -MID_COUNT: 1 -MID_SEQ: CTACGCTCTA ---- -REC_TYPE: MID -MID_NUM: 61 -MID_COUNT: 1 -MID_SEQ: CTATAGCGTA ---- -REC_TYPE: MID -MID_NUM: 62 -MID_COUNT: 1 -MID_SEQ: TACGTCATCA ---- -REC_TYPE: MID -MID_NUM: 63 -MID_COUNT: 1 -MID_SEQ: TAGTCGCATA ---- -REC_TYPE: MID -MID_NUM: 64 -MID_COUNT: 1 -MID_SEQ: TATATATACA ---- -REC_TYPE: MID -MID_NUM: 65 -MID_COUNT: 1 -MID_SEQ: TATGCTAGTA ---- -REC_TYPE: MID -MID_NUM: 66 -MID_COUNT: 1 -MID_SEQ: TCACGCGAGA ---- -REC_TYPE: MID -MID_NUM: 67 -MID_COUNT: 1 -MID_SEQ: TCGATAGTGA ---- -REC_TYPE: MID -MID_NUM: 68 -MID_COUNT: 1 -MID_SEQ: TCGCTGCGTA ---- -REC_TYPE: MID -MID_NUM: 69 -MID_COUNT: 1 -MID_SEQ: TCTGACGTCA ---- -REC_TYPE: MID -MID_NUM: 70 -MID_COUNT: 1 -MID_SEQ: TGAGTCAGTA ---- -REC_TYPE: MID -MID_NUM: 71 -MID_COUNT: 1 -MID_SEQ: TGTAGTGTGA ---- -REC_TYPE: MID -MID_NUM: 72 -MID_COUNT: 1 -MID_SEQ: TGTCACACGA ---- -REC_TYPE: MID -MID_NUM: 73 -MID_COUNT: 1 -MID_SEQ: TGTCGTCGCA ---- -REC_TYPE: MID -MID_NUM: 74 -MID_COUNT: 1 -MID_SEQ: ACACATACGC ---- -REC_TYPE: MID -MID_NUM: 75 -MID_COUNT: 1 -MID_SEQ: ACAGTCGTGC ---- -REC_TYPE: MID -MID_NUM: 76 -MID_COUNT: 1 -MID_SEQ: ACATGACGAC ---- -REC_TYPE: MID -MID_NUM: 77 -MID_COUNT: 1 -MID_SEQ: ACGACAGCTC ---- -REC_TYPE: MID -MID_NUM: 78 -MID_COUNT: 1 -MID_SEQ: ACGTCTCATC ---- -REC_TYPE: MID -MID_NUM: 79 -MID_COUNT: 1 -MID_SEQ: ACTCATCTAC ---- -REC_TYPE: MID -MID_NUM: 80 -MID_COUNT: 1 -MID_SEQ: ACTCGCGCAC ---- -REC_TYPE: MID -MID_NUM: 81 -MID_COUNT: 1 -MID_SEQ: AGAGCGTCAC ---- -REC_TYPE: MID -MID_NUM: 82 -MID_COUNT: 1 -MID_SEQ: AGCGACTAGC ---- -REC_TYPE: MID -MID_NUM: 83 -MID_COUNT: 1 -MID_SEQ: AGTAGTGATC ---- -REC_TYPE: MID -MID_NUM: 84 -MID_COUNT: 1 -MID_SEQ: AGTGACACAC ---- -REC_TYPE: MID -MID_NUM: 85 -MID_COUNT: 1 -MID_SEQ: AGTGTATGTC ---- -REC_TYPE: MID -MID_NUM: 86 -MID_COUNT: 1 -MID_SEQ: ATAGATAGAC ---- -REC_TYPE: MID -MID_NUM: 87 -MID_COUNT: 1 -MID_SEQ: ATATAGTCGC ---- -REC_TYPE: MID -MID_NUM: 88 -MID_COUNT: 1 -MID_SEQ: ATCTACTGAC ---- -REC_TYPE: MID -MID_NUM: 89 -MID_COUNT: 1 -MID_SEQ: CACGTAGATC ---- -REC_TYPE: MID -MID_NUM: 90 -MID_COUNT: 1 -MID_SEQ: CACGTGTCGC ---- -REC_TYPE: MID -MID_NUM: 91 -MID_COUNT: 1 -MID_SEQ: CATACTCTAC ---- -REC_TYPE: MID -MID_NUM: 92 -MID_COUNT: 1 -MID_SEQ: CGACACTATC ---- -REC_TYPE: MID -MID_NUM: 93 -MID_COUNT: 1 -MID_SEQ: CGAGACGCGC ---- -REC_TYPE: MID -MID_NUM: 94 -MID_COUNT: 1 -MID_SEQ: CGTATGCGAC ---- -REC_TYPE: MID -MID_NUM: 95 -MID_COUNT: 1 -MID_SEQ: CGTCGATCTC ---- -REC_TYPE: MID -MID_NUM: 96 -MID_COUNT: 1 -MID_SEQ: CTACGACTGC ---- -REC_TYPE: MID -MID_NUM: 97 -MID_COUNT: 1 -MID_SEQ: CTAGTCACTC ---- -REC_TYPE: MID -MID_NUM: 98 -MID_COUNT: 1 -MID_SEQ: CTCTACGCTC ---- -REC_TYPE: MID -MID_NUM: 99 -MID_COUNT: 1 -MID_SEQ: CTGTACATAC ---- -REC_TYPE: MID -MID_NUM: 100 -MID_COUNT: 1 -MID_SEQ: TAGACTGCAC ---- -REC_TYPE: MID -MID_NUM: 101 -MID_COUNT: 1 -MID_SEQ: TAGCGCGCGC ---- -REC_TYPE: MID -MID_NUM: 102 -MID_COUNT: 1 -MID_SEQ: TAGCTCTATC ---- -REC_TYPE: MID -MID_NUM: 103 -MID_COUNT: 1 -MID_SEQ: TATAGACATC ---- -REC_TYPE: MID -MID_NUM: 104 -MID_COUNT: 1 -MID_SEQ: TATGATACGC ---- -REC_TYPE: MID -MID_NUM: 105 -MID_COUNT: 1 -MID_SEQ: TCACTCATAC ---- -REC_TYPE: MID -MID_NUM: 106 -MID_COUNT: 1 -MID_SEQ: TCATCGAGTC ---- -REC_TYPE: MID -MID_NUM: 107 -MID_COUNT: 1 -MID_SEQ: TCGAGCTCTC ---- -REC_TYPE: MID -MID_NUM: 108 -MID_COUNT: 1 -MID_SEQ: TCGCAGACAC ---- -REC_TYPE: MID -MID_NUM: 109 -MID_COUNT: 1 -MID_SEQ: TCTGTCTCGC ---- -REC_TYPE: MID -MID_NUM: 110 -MID_COUNT: 1 -MID_SEQ: TGAGTGACGC ---- -REC_TYPE: MID -MID_NUM: 111 -MID_COUNT: 1 -MID_SEQ: TGATGTGTAC ---- -REC_TYPE: MID -MID_NUM: 112 -MID_COUNT: 1 -MID_SEQ: TGCTATAGAC ---- -REC_TYPE: MID -MID_NUM: 113 -MID_COUNT: 1 -MID_SEQ: TGCTCGCTAC ---- -REC_TYPE: MID -MID_NUM: 114 -MID_COUNT: 1 -MID_SEQ: ACGTGCAGCG ---- -REC_TYPE: MID -MID_NUM: 115 -MID_COUNT: 1 -MID_SEQ: ACTCACAGAG ---- -REC_TYPE: MID -MID_NUM: 116 -MID_COUNT: 1 -MID_SEQ: AGACTCAGCG ---- -REC_TYPE: MID -MID_NUM: 117 -MID_COUNT: 1 -MID_SEQ: AGAGAGTGTG ---- -REC_TYPE: MID -MID_NUM: 118 -MID_COUNT: 1 -MID_SEQ: AGCTATCGCG ---- -REC_TYPE: MID -MID_NUM: 119 -MID_COUNT: 1 -MID_SEQ: AGTCTGACTG ---- -REC_TYPE: MID -MID_NUM: 120 -MID_COUNT: 1 -MID_SEQ: AGTGAGCTCG ---- -REC_TYPE: MID -MID_NUM: 121 -MID_COUNT: 1 -MID_SEQ: ATAGCTCTCG ---- -REC_TYPE: MID -MID_NUM: 122 -MID_COUNT: 1 -MID_SEQ: ATCACGTGCG ---- -REC_TYPE: MID -MID_NUM: 123 -MID_COUNT: 1 -MID_SEQ: ATCGTAGCAG ---- -REC_TYPE: MID -MID_NUM: 124 -MID_COUNT: 1 -MID_SEQ: ATCGTCTGTG ---- -REC_TYPE: MID -MID_NUM: 125 -MID_COUNT: 1 -MID_SEQ: ATGTACGATG ---- -REC_TYPE: MID -MID_NUM: 126 -MID_COUNT: 1 -MID_SEQ: ATGTGTCTAG ---- -REC_TYPE: MID -MID_NUM: 127 -MID_COUNT: 1 -MID_SEQ: CACACGATAG ---- -REC_TYPE: MID -MID_NUM: 128 -MID_COUNT: 1 -MID_SEQ: CACTCGCACG ---- -REC_TYPE: MID -MID_NUM: 129 -MID_COUNT: 1 -MID_SEQ: CAGACGTCTG ---- -REC_TYPE: MID -MID_NUM: 130 -MID_COUNT: 1 -MID_SEQ: CAGTACTGCG ---- -REC_TYPE: MID -MID_NUM: 131 -MID_COUNT: 1 -MID_SEQ: CGACAGCGAG ---- -REC_TYPE: MID -MID_NUM: 132 -MID_COUNT: 1 -MID_SEQ: CGATCTGTCG ---- -REC_TYPE: MID -MID_NUM: 133 -MID_COUNT: 1 -MID_SEQ: CGCGTGCTAG ---- -REC_TYPE: MID -MID_NUM: 134 -MID_COUNT: 1 -MID_SEQ: CGCTCGAGTG ---- -REC_TYPE: MID -MID_NUM: 135 -MID_COUNT: 1 -MID_SEQ: CGTGATGACG ---- -REC_TYPE: MID -MID_NUM: 136 -MID_COUNT: 1 -MID_SEQ: CTATGTACAG ---- -REC_TYPE: MID -MID_NUM: 137 -MID_COUNT: 1 -MID_SEQ: CTCGATATAG ---- -REC_TYPE: MID -MID_NUM: 138 -MID_COUNT: 1 -MID_SEQ: CTCGCACGCG ---- -REC_TYPE: MID -MID_NUM: 139 -MID_COUNT: 1 -MID_SEQ: CTGCGTCACG ---- -REC_TYPE: MID -MID_NUM: 140 -MID_COUNT: 1 -MID_SEQ: CTGTGCGTCG ---- -REC_TYPE: MID -MID_NUM: 141 -MID_COUNT: 1 -MID_SEQ: TAGCATACTG ---- -REC_TYPE: MID -MID_NUM: 142 -MID_COUNT: 1 -MID_SEQ: TATACATGTG ---- -REC_TYPE: MID -MID_NUM: 143 -MID_COUNT: 1 -MID_SEQ: TATCACTCAG ---- -REC_TYPE: MID -MID_NUM: 144 -MID_COUNT: 1 -MID_SEQ: TATCTGATAG ---- -REC_TYPE: MID -MID_NUM: 145 -MID_COUNT: 1 -MID_SEQ: TCGTGACATG ---- -REC_TYPE: MID -MID_NUM: 146 -MID_COUNT: 1 -MID_SEQ: TCTGATCGAG ---- -REC_TYPE: MID -MID_NUM: 147 -MID_COUNT: 1 -MID_SEQ: TGACATCTCG ---- -REC_TYPE: MID -MID_NUM: 148 -MID_COUNT: 1 -MID_SEQ: TGAGCTAGAG ---- -REC_TYPE: MID -MID_NUM: 149 -MID_COUNT: 1 -MID_SEQ: TGATAGAGCG ---- -REC_TYPE: MID -MID_NUM: 150 -MID_COUNT: 1 -MID_SEQ: TGCGTGTGCG ---- -REC_TYPE: MID -MID_NUM: 151 -MID_COUNT: 1 -MID_SEQ: TGCTAGTCAG ---- -REC_TYPE: MID -MID_NUM: 152 -MID_COUNT: 1 -MID_SEQ: TGTATCACAG ---- -REC_TYPE: MID -MID_NUM: 153 -MID_COUNT: 1 -MID_SEQ: TGTGCGCGTG ---- diff --git a/bp_test/out/find_mids.out.2 b/bp_test/out/find_mids.out.2 deleted file mode 100644 index 04b2578..0000000 --- a/bp_test/out/find_mids.out.2 +++ /dev/null @@ -1,1071 +0,0 @@ -SEQ: ACGAGTGCGTatcg ---- -SEQ: ACGCTCGACAatcg ---- -SEQ: AGACGCACTCatcg ---- -SEQ: AGCACTGTAGatcg ---- -SEQ: ATCAGACACGatcg ---- -SEQ: ATATCGCGAGatcg ---- -SEQ: CGTGTCTCTAatcg ---- -SEQ: CTCGCGTGTCatcg ---- -SEQ: TAGTATCAGCatcg ---- -SEQ: TCTCTATGCGatcg ---- -SEQ: TGATACGTCTatcg ---- -SEQ: TACTGAGCTAatcg ---- -SEQ: CATAGTAGTGatcg ---- -SEQ: CGAGAGATACatcg ---- -SEQ: ATACGACGTAatcg ---- -SEQ: TCACGTACTAatcg ---- -SEQ: CGTCTAGTACatcg ---- -SEQ: TCTACGTAGCatcg ---- -SEQ: TGTACTACTCatcg ---- -SEQ: ACGACTACAGatcg ---- -SEQ: CGTAGACTAGatcg ---- -SEQ: TACGAGTATGatcg ---- -SEQ: TACTCTCGTGatcg ---- -SEQ: TAGAGACGAGatcg ---- -SEQ: TCGTCGCTCGatcg ---- -SEQ: ACATACGCGTatcg ---- -SEQ: ACGCGAGTATatcg ---- -SEQ: ACTACTATGTatcg ---- -SEQ: ACTGTACAGTatcg ---- -SEQ: AGACTATACTatcg ---- -SEQ: AGCGTCGTCTatcg ---- -SEQ: AGTACGCTATatcg ---- -SEQ: ATAGAGTACTatcg ---- -SEQ: CACGCTACGTatcg ---- -SEQ: CAGTAGACGTatcg ---- -SEQ: CGACGTGACTatcg ---- -SEQ: TACACACACTatcg ---- -SEQ: TACACGTGATatcg ---- -SEQ: TACAGATCGTatcg ---- -SEQ: TACGCTGTCTatcg ---- -SEQ: TAGTGTAGATatcg ---- -SEQ: TCGATCACGTatcg ---- -SEQ: TCGCACTAGTatcg ---- -SEQ: TCTAGCGACTatcg ---- -SEQ: TCTATACTATatcg ---- -SEQ: TGACGTATGTatcg ---- -SEQ: TGTGAGTAGTatcg ---- -SEQ: ACAGTATATAatcg ---- -SEQ: ACGCGATCGAatcg ---- -SEQ: ACTAGCAGTAatcg ---- -SEQ: AGCTCACGTAatcg ---- -SEQ: AGTATACATAatcg ---- -SEQ: AGTCGAGAGAatcg ---- -SEQ: AGTGCTACGAatcg ---- -SEQ: CGATCGTATAatcg ---- -SEQ: CGCAGTACGAatcg ---- -SEQ: CGCGTATACAatcg ---- -SEQ: CGTACAGTCAatcg ---- -SEQ: CGTACTCAGAatcg ---- -SEQ: CTACGCTCTAatcg ---- -SEQ: CTATAGCGTAatcg ---- -SEQ: TACGTCATCAatcg ---- -SEQ: TAGTCGCATAatcg ---- -SEQ: TATATATACAatcg ---- -SEQ: TATGCTAGTAatcg ---- -SEQ: TCACGCGAGAatcg ---- -SEQ: TCGATAGTGAatcg ---- -SEQ: TCGCTGCGTAatcg ---- -SEQ: TCTGACGTCAatcg ---- -SEQ: TGAGTCAGTAatcg ---- -SEQ: TGTAGTGTGAatcg ---- -SEQ: TGTCACACGAatcg ---- -SEQ: TGTCGTCGCAatcg ---- -SEQ: ACACATACGCatcg ---- -SEQ: ACAGTCGTGCatcg ---- -SEQ: ACATGACGACatcg ---- -SEQ: ACGACAGCTCatcg ---- -SEQ: ACGTCTCATCatcg ---- -SEQ: ACTCATCTACatcg ---- -SEQ: ACTCGCGCACatcg ---- -SEQ: AGAGCGTCACatcg ---- -SEQ: AGCGACTAGCatcg ---- -SEQ: AGTAGTGATCatcg ---- -SEQ: AGTGACACACatcg ---- -SEQ: AGTGTATGTCatcg ---- -SEQ: ATAGATAGACatcg ---- -SEQ: ATATAGTCGCatcg ---- -SEQ: ATCTACTGACatcg ---- -SEQ: CACGTAGATCatcg ---- -SEQ: CACGTGTCGCatcg ---- -SEQ: CATACTCTACatcg ---- -SEQ: CGACACTATCatcg ---- -SEQ: CGAGACGCGCatcg ---- -SEQ: CGTATGCGACatcg ---- -SEQ: CGTCGATCTCatcg ---- -SEQ: CTACGACTGCatcg ---- -SEQ: CTAGTCACTCatcg ---- -SEQ: CTCTACGCTCatcg ---- -SEQ: CTGTACATACatcg ---- -SEQ: TAGACTGCACatcg ---- -SEQ: TAGCGCGCGCatcg ---- -SEQ: TAGCTCTATCatcg ---- -SEQ: TATAGACATCatcg ---- -SEQ: TATGATACGCatcg ---- -SEQ: TCACTCATACatcg ---- -SEQ: TCATCGAGTCatcg ---- -SEQ: TCGAGCTCTCatcg ---- -SEQ: TCGCAGACACatcg ---- -SEQ: TCTGTCTCGCatcg ---- -SEQ: TGAGTGACGCatcg ---- -SEQ: TGATGTGTACatcg ---- -SEQ: TGCTATAGACatcg ---- -SEQ: TGCTCGCTACatcg ---- -SEQ: ACGTGCAGCGatcg ---- -SEQ: ACTCACAGAGatcg ---- -SEQ: AGACTCAGCGatcg ---- -SEQ: AGAGAGTGTGatcg ---- -SEQ: AGCTATCGCGatcg ---- -SEQ: AGTCTGACTGatcg ---- -SEQ: AGTGAGCTCGatcg ---- -SEQ: ATAGCTCTCGatcg ---- -SEQ: ATCACGTGCGatcg ---- -SEQ: ATCGTAGCAGatcg ---- -SEQ: ATCGTCTGTGatcg ---- -SEQ: ATGTACGATGatcg ---- -SEQ: ATGTGTCTAGatcg ---- -SEQ: CACACGATAGatcg ---- -SEQ: CACTCGCACGatcg ---- -SEQ: CAGACGTCTGatcg ---- -SEQ: CAGTACTGCGatcg ---- -SEQ: CGACAGCGAGatcg ---- -SEQ: CGATCTGTCGatcg ---- -SEQ: CGCGTGCTAGatcg ---- -SEQ: CGCTCGAGTGatcg ---- -SEQ: CGTGATGACGatcg ---- -SEQ: CTATGTACAGatcg ---- -SEQ: CTCGATATAGatcg ---- -SEQ: CTCGCACGCGatcg ---- -SEQ: CTGCGTCACGatcg ---- -SEQ: CTGTGCGTCGatcg ---- -SEQ: TAGCATACTGatcg ---- -SEQ: TATACATGTGatcg ---- -SEQ: TATCACTCAGatcg ---- -SEQ: TATCTGATAGatcg ---- -SEQ: TCGTGACATGatcg ---- -SEQ: TCTGATCGAGatcg ---- -SEQ: TGACATCTCGatcg ---- -SEQ: TGAGCTAGAGatcg ---- -SEQ: TGATAGAGCGatcg ---- -SEQ: TGCGTGTGCGatcg ---- -SEQ: TGCTAGTCAGatcg ---- -SEQ: TGTATCACAGatcg ---- -SEQ: TGTGCGCGTGatcg ---- -REC_TYPE: MID -MID_NUM: 1 -MID_COUNT: 1 -MID_SEQ: ACGAGTGCGT ---- -REC_TYPE: MID -MID_NUM: 2 -MID_COUNT: 1 -MID_SEQ: ACGCTCGACA ---- -REC_TYPE: MID -MID_NUM: 3 -MID_COUNT: 1 -MID_SEQ: AGACGCACTC ---- -REC_TYPE: MID -MID_NUM: 4 -MID_COUNT: 1 -MID_SEQ: AGCACTGTAG ---- -REC_TYPE: MID -MID_NUM: 5 -MID_COUNT: 1 -MID_SEQ: ATCAGACACG ---- -REC_TYPE: MID -MID_NUM: 6 -MID_COUNT: 1 -MID_SEQ: ATATCGCGAG ---- -REC_TYPE: MID -MID_NUM: 7 -MID_COUNT: 1 -MID_SEQ: CGTGTCTCTA ---- -REC_TYPE: MID -MID_NUM: 8 -MID_COUNT: 1 -MID_SEQ: CTCGCGTGTC ---- -REC_TYPE: MID -MID_NUM: 9 -MID_COUNT: 1 -MID_SEQ: TAGTATCAGC ---- -REC_TYPE: MID -MID_NUM: 10 -MID_COUNT: 1 -MID_SEQ: TCTCTATGCG ---- -REC_TYPE: MID -MID_NUM: 11 -MID_COUNT: 1 -MID_SEQ: TGATACGTCT ---- -REC_TYPE: MID -MID_NUM: 12 -MID_COUNT: 1 -MID_SEQ: TACTGAGCTA ---- -REC_TYPE: MID -MID_NUM: 13 -MID_COUNT: 1 -MID_SEQ: CATAGTAGTG ---- -REC_TYPE: MID -MID_NUM: 14 -MID_COUNT: 1 -MID_SEQ: CGAGAGATAC ---- -REC_TYPE: MID -MID_NUM: 15 -MID_COUNT: 1 -MID_SEQ: ATACGACGTA ---- -REC_TYPE: MID -MID_NUM: 16 -MID_COUNT: 1 -MID_SEQ: TCACGTACTA ---- -REC_TYPE: MID -MID_NUM: 17 -MID_COUNT: 1 -MID_SEQ: CGTCTAGTAC ---- -REC_TYPE: MID -MID_NUM: 18 -MID_COUNT: 1 -MID_SEQ: TCTACGTAGC ---- -REC_TYPE: MID -MID_NUM: 19 -MID_COUNT: 1 -MID_SEQ: TGTACTACTC ---- -REC_TYPE: MID -MID_NUM: 20 -MID_COUNT: 1 -MID_SEQ: ACGACTACAG ---- -REC_TYPE: MID -MID_NUM: 21 -MID_COUNT: 1 -MID_SEQ: CGTAGACTAG ---- -REC_TYPE: MID -MID_NUM: 22 -MID_COUNT: 1 -MID_SEQ: TACGAGTATG ---- -REC_TYPE: MID -MID_NUM: 23 -MID_COUNT: 1 -MID_SEQ: TACTCTCGTG ---- -REC_TYPE: MID -MID_NUM: 24 -MID_COUNT: 1 -MID_SEQ: TAGAGACGAG ---- -REC_TYPE: MID -MID_NUM: 25 -MID_COUNT: 1 -MID_SEQ: TCGTCGCTCG ---- -REC_TYPE: MID -MID_NUM: 26 -MID_COUNT: 1 -MID_SEQ: ACATACGCGT ---- -REC_TYPE: MID -MID_NUM: 27 -MID_COUNT: 1 -MID_SEQ: ACGCGAGTAT ---- -REC_TYPE: MID -MID_NUM: 28 -MID_COUNT: 1 -MID_SEQ: ACTACTATGT ---- -REC_TYPE: MID -MID_NUM: 29 -MID_COUNT: 1 -MID_SEQ: ACTGTACAGT ---- -REC_TYPE: MID -MID_NUM: 30 -MID_COUNT: 1 -MID_SEQ: AGACTATACT ---- -REC_TYPE: MID -MID_NUM: 31 -MID_COUNT: 1 -MID_SEQ: AGCGTCGTCT ---- -REC_TYPE: MID -MID_NUM: 32 -MID_COUNT: 1 -MID_SEQ: AGTACGCTAT ---- -REC_TYPE: MID -MID_NUM: 33 -MID_COUNT: 1 -MID_SEQ: ATAGAGTACT ---- -REC_TYPE: MID -MID_NUM: 34 -MID_COUNT: 1 -MID_SEQ: CACGCTACGT ---- -REC_TYPE: MID -MID_NUM: 35 -MID_COUNT: 1 -MID_SEQ: CAGTAGACGT ---- -REC_TYPE: MID -MID_NUM: 36 -MID_COUNT: 1 -MID_SEQ: CGACGTGACT ---- -REC_TYPE: MID -MID_NUM: 37 -MID_COUNT: 1 -MID_SEQ: TACACACACT ---- -REC_TYPE: MID -MID_NUM: 38 -MID_COUNT: 1 -MID_SEQ: TACACGTGAT ---- -REC_TYPE: MID -MID_NUM: 39 -MID_COUNT: 1 -MID_SEQ: TACAGATCGT ---- -REC_TYPE: MID -MID_NUM: 40 -MID_COUNT: 1 -MID_SEQ: TACGCTGTCT ---- -REC_TYPE: MID -MID_NUM: 41 -MID_COUNT: 1 -MID_SEQ: TAGTGTAGAT ---- -REC_TYPE: MID -MID_NUM: 42 -MID_COUNT: 1 -MID_SEQ: TCGATCACGT ---- -REC_TYPE: MID -MID_NUM: 43 -MID_COUNT: 1 -MID_SEQ: TCGCACTAGT ---- -REC_TYPE: MID -MID_NUM: 44 -MID_COUNT: 1 -MID_SEQ: TCTAGCGACT ---- -REC_TYPE: MID -MID_NUM: 45 -MID_COUNT: 1 -MID_SEQ: TCTATACTAT ---- -REC_TYPE: MID -MID_NUM: 46 -MID_COUNT: 1 -MID_SEQ: TGACGTATGT ---- -REC_TYPE: MID -MID_NUM: 47 -MID_COUNT: 1 -MID_SEQ: TGTGAGTAGT ---- -REC_TYPE: MID -MID_NUM: 48 -MID_COUNT: 1 -MID_SEQ: ACAGTATATA ---- -REC_TYPE: MID -MID_NUM: 49 -MID_COUNT: 1 -MID_SEQ: ACGCGATCGA ---- -REC_TYPE: MID -MID_NUM: 50 -MID_COUNT: 1 -MID_SEQ: ACTAGCAGTA ---- -REC_TYPE: MID -MID_NUM: 51 -MID_COUNT: 1 -MID_SEQ: AGCTCACGTA ---- -REC_TYPE: MID -MID_NUM: 52 -MID_COUNT: 1 -MID_SEQ: AGTATACATA ---- -REC_TYPE: MID -MID_NUM: 53 -MID_COUNT: 1 -MID_SEQ: AGTCGAGAGA ---- -REC_TYPE: MID -MID_NUM: 54 -MID_COUNT: 1 -MID_SEQ: AGTGCTACGA ---- -REC_TYPE: MID -MID_NUM: 55 -MID_COUNT: 1 -MID_SEQ: CGATCGTATA ---- -REC_TYPE: MID -MID_NUM: 56 -MID_COUNT: 1 -MID_SEQ: CGCAGTACGA ---- -REC_TYPE: MID -MID_NUM: 57 -MID_COUNT: 1 -MID_SEQ: CGCGTATACA ---- -REC_TYPE: MID -MID_NUM: 58 -MID_COUNT: 1 -MID_SEQ: CGTACAGTCA ---- -REC_TYPE: MID -MID_NUM: 59 -MID_COUNT: 1 -MID_SEQ: CGTACTCAGA ---- -REC_TYPE: MID -MID_NUM: 60 -MID_COUNT: 1 -MID_SEQ: CTACGCTCTA ---- -REC_TYPE: MID -MID_NUM: 61 -MID_COUNT: 1 -MID_SEQ: CTATAGCGTA ---- -REC_TYPE: MID -MID_NUM: 62 -MID_COUNT: 1 -MID_SEQ: TACGTCATCA ---- -REC_TYPE: MID -MID_NUM: 63 -MID_COUNT: 1 -MID_SEQ: TAGTCGCATA ---- -REC_TYPE: MID -MID_NUM: 64 -MID_COUNT: 1 -MID_SEQ: TATATATACA ---- -REC_TYPE: MID -MID_NUM: 65 -MID_COUNT: 1 -MID_SEQ: TATGCTAGTA ---- -REC_TYPE: MID -MID_NUM: 66 -MID_COUNT: 1 -MID_SEQ: TCACGCGAGA ---- -REC_TYPE: MID -MID_NUM: 67 -MID_COUNT: 1 -MID_SEQ: TCGATAGTGA ---- -REC_TYPE: MID -MID_NUM: 68 -MID_COUNT: 1 -MID_SEQ: TCGCTGCGTA ---- -REC_TYPE: MID -MID_NUM: 69 -MID_COUNT: 1 -MID_SEQ: TCTGACGTCA ---- -REC_TYPE: MID -MID_NUM: 70 -MID_COUNT: 1 -MID_SEQ: TGAGTCAGTA ---- -REC_TYPE: MID -MID_NUM: 71 -MID_COUNT: 1 -MID_SEQ: TGTAGTGTGA ---- -REC_TYPE: MID -MID_NUM: 72 -MID_COUNT: 1 -MID_SEQ: TGTCACACGA ---- -REC_TYPE: MID -MID_NUM: 73 -MID_COUNT: 1 -MID_SEQ: TGTCGTCGCA ---- -REC_TYPE: MID -MID_NUM: 74 -MID_COUNT: 1 -MID_SEQ: ACACATACGC ---- -REC_TYPE: MID -MID_NUM: 75 -MID_COUNT: 1 -MID_SEQ: ACAGTCGTGC ---- -REC_TYPE: MID -MID_NUM: 76 -MID_COUNT: 1 -MID_SEQ: ACATGACGAC ---- -REC_TYPE: MID -MID_NUM: 77 -MID_COUNT: 1 -MID_SEQ: ACGACAGCTC ---- -REC_TYPE: MID -MID_NUM: 78 -MID_COUNT: 1 -MID_SEQ: ACGTCTCATC ---- -REC_TYPE: MID -MID_NUM: 79 -MID_COUNT: 1 -MID_SEQ: ACTCATCTAC ---- -REC_TYPE: MID -MID_NUM: 80 -MID_COUNT: 1 -MID_SEQ: ACTCGCGCAC ---- -REC_TYPE: MID -MID_NUM: 81 -MID_COUNT: 1 -MID_SEQ: AGAGCGTCAC ---- -REC_TYPE: MID -MID_NUM: 82 -MID_COUNT: 1 -MID_SEQ: AGCGACTAGC ---- -REC_TYPE: MID -MID_NUM: 83 -MID_COUNT: 1 -MID_SEQ: AGTAGTGATC ---- -REC_TYPE: MID -MID_NUM: 84 -MID_COUNT: 1 -MID_SEQ: AGTGACACAC ---- -REC_TYPE: MID -MID_NUM: 85 -MID_COUNT: 1 -MID_SEQ: AGTGTATGTC ---- -REC_TYPE: MID -MID_NUM: 86 -MID_COUNT: 1 -MID_SEQ: ATAGATAGAC ---- -REC_TYPE: MID -MID_NUM: 87 -MID_COUNT: 1 -MID_SEQ: ATATAGTCGC ---- -REC_TYPE: MID -MID_NUM: 88 -MID_COUNT: 1 -MID_SEQ: ATCTACTGAC ---- -REC_TYPE: MID -MID_NUM: 89 -MID_COUNT: 1 -MID_SEQ: CACGTAGATC ---- -REC_TYPE: MID -MID_NUM: 90 -MID_COUNT: 1 -MID_SEQ: CACGTGTCGC ---- -REC_TYPE: MID -MID_NUM: 91 -MID_COUNT: 1 -MID_SEQ: CATACTCTAC ---- -REC_TYPE: MID -MID_NUM: 92 -MID_COUNT: 1 -MID_SEQ: CGACACTATC ---- -REC_TYPE: MID -MID_NUM: 93 -MID_COUNT: 1 -MID_SEQ: CGAGACGCGC ---- -REC_TYPE: MID -MID_NUM: 94 -MID_COUNT: 1 -MID_SEQ: CGTATGCGAC ---- -REC_TYPE: MID -MID_NUM: 95 -MID_COUNT: 1 -MID_SEQ: CGTCGATCTC ---- -REC_TYPE: MID -MID_NUM: 96 -MID_COUNT: 1 -MID_SEQ: CTACGACTGC ---- -REC_TYPE: MID -MID_NUM: 97 -MID_COUNT: 1 -MID_SEQ: CTAGTCACTC ---- -REC_TYPE: MID -MID_NUM: 98 -MID_COUNT: 1 -MID_SEQ: CTCTACGCTC ---- -REC_TYPE: MID -MID_NUM: 99 -MID_COUNT: 1 -MID_SEQ: CTGTACATAC ---- -REC_TYPE: MID -MID_NUM: 100 -MID_COUNT: 1 -MID_SEQ: TAGACTGCAC ---- -REC_TYPE: MID -MID_NUM: 101 -MID_COUNT: 1 -MID_SEQ: TAGCGCGCGC ---- -REC_TYPE: MID -MID_NUM: 102 -MID_COUNT: 1 -MID_SEQ: TAGCTCTATC ---- -REC_TYPE: MID -MID_NUM: 103 -MID_COUNT: 1 -MID_SEQ: TATAGACATC ---- -REC_TYPE: MID -MID_NUM: 104 -MID_COUNT: 1 -MID_SEQ: TATGATACGC ---- -REC_TYPE: MID -MID_NUM: 105 -MID_COUNT: 1 -MID_SEQ: TCACTCATAC ---- -REC_TYPE: MID -MID_NUM: 106 -MID_COUNT: 1 -MID_SEQ: TCATCGAGTC ---- -REC_TYPE: MID -MID_NUM: 107 -MID_COUNT: 1 -MID_SEQ: TCGAGCTCTC ---- -REC_TYPE: MID -MID_NUM: 108 -MID_COUNT: 1 -MID_SEQ: TCGCAGACAC ---- -REC_TYPE: MID -MID_NUM: 109 -MID_COUNT: 1 -MID_SEQ: TCTGTCTCGC ---- -REC_TYPE: MID -MID_NUM: 110 -MID_COUNT: 1 -MID_SEQ: TGAGTGACGC ---- -REC_TYPE: MID -MID_NUM: 111 -MID_COUNT: 1 -MID_SEQ: TGATGTGTAC ---- -REC_TYPE: MID -MID_NUM: 112 -MID_COUNT: 1 -MID_SEQ: TGCTATAGAC ---- -REC_TYPE: MID -MID_NUM: 113 -MID_COUNT: 1 -MID_SEQ: TGCTCGCTAC ---- -REC_TYPE: MID -MID_NUM: 114 -MID_COUNT: 1 -MID_SEQ: ACGTGCAGCG ---- -REC_TYPE: MID -MID_NUM: 115 -MID_COUNT: 1 -MID_SEQ: ACTCACAGAG ---- -REC_TYPE: MID -MID_NUM: 116 -MID_COUNT: 1 -MID_SEQ: AGACTCAGCG ---- -REC_TYPE: MID -MID_NUM: 117 -MID_COUNT: 1 -MID_SEQ: AGAGAGTGTG ---- -REC_TYPE: MID -MID_NUM: 118 -MID_COUNT: 1 -MID_SEQ: AGCTATCGCG ---- -REC_TYPE: MID -MID_NUM: 119 -MID_COUNT: 1 -MID_SEQ: AGTCTGACTG ---- -REC_TYPE: MID -MID_NUM: 120 -MID_COUNT: 1 -MID_SEQ: AGTGAGCTCG ---- -REC_TYPE: MID -MID_NUM: 121 -MID_COUNT: 1 -MID_SEQ: ATAGCTCTCG ---- -REC_TYPE: MID -MID_NUM: 122 -MID_COUNT: 1 -MID_SEQ: ATCACGTGCG ---- -REC_TYPE: MID -MID_NUM: 123 -MID_COUNT: 1 -MID_SEQ: ATCGTAGCAG ---- -REC_TYPE: MID -MID_NUM: 124 -MID_COUNT: 1 -MID_SEQ: ATCGTCTGTG ---- -REC_TYPE: MID -MID_NUM: 125 -MID_COUNT: 1 -MID_SEQ: ATGTACGATG ---- -REC_TYPE: MID -MID_NUM: 126 -MID_COUNT: 1 -MID_SEQ: ATGTGTCTAG ---- -REC_TYPE: MID -MID_NUM: 127 -MID_COUNT: 1 -MID_SEQ: CACACGATAG ---- -REC_TYPE: MID -MID_NUM: 128 -MID_COUNT: 1 -MID_SEQ: CACTCGCACG ---- -REC_TYPE: MID -MID_NUM: 129 -MID_COUNT: 1 -MID_SEQ: CAGACGTCTG ---- -REC_TYPE: MID -MID_NUM: 130 -MID_COUNT: 1 -MID_SEQ: CAGTACTGCG ---- -REC_TYPE: MID -MID_NUM: 131 -MID_COUNT: 1 -MID_SEQ: CGACAGCGAG ---- -REC_TYPE: MID -MID_NUM: 132 -MID_COUNT: 1 -MID_SEQ: CGATCTGTCG ---- -REC_TYPE: MID -MID_NUM: 133 -MID_COUNT: 1 -MID_SEQ: CGCGTGCTAG ---- -REC_TYPE: MID -MID_NUM: 134 -MID_COUNT: 1 -MID_SEQ: CGCTCGAGTG ---- -REC_TYPE: MID -MID_NUM: 135 -MID_COUNT: 1 -MID_SEQ: CGTGATGACG ---- -REC_TYPE: MID -MID_NUM: 136 -MID_COUNT: 1 -MID_SEQ: CTATGTACAG ---- -REC_TYPE: MID -MID_NUM: 137 -MID_COUNT: 1 -MID_SEQ: CTCGATATAG ---- -REC_TYPE: MID -MID_NUM: 138 -MID_COUNT: 1 -MID_SEQ: CTCGCACGCG ---- -REC_TYPE: MID -MID_NUM: 139 -MID_COUNT: 1 -MID_SEQ: CTGCGTCACG ---- -REC_TYPE: MID -MID_NUM: 140 -MID_COUNT: 1 -MID_SEQ: CTGTGCGTCG ---- -REC_TYPE: MID -MID_NUM: 141 -MID_COUNT: 1 -MID_SEQ: TAGCATACTG ---- -REC_TYPE: MID -MID_NUM: 142 -MID_COUNT: 1 -MID_SEQ: TATACATGTG ---- -REC_TYPE: MID -MID_NUM: 143 -MID_COUNT: 1 -MID_SEQ: TATCACTCAG ---- -REC_TYPE: MID -MID_NUM: 144 -MID_COUNT: 1 -MID_SEQ: TATCTGATAG ---- -REC_TYPE: MID -MID_NUM: 145 -MID_COUNT: 1 -MID_SEQ: TCGTGACATG ---- -REC_TYPE: MID -MID_NUM: 146 -MID_COUNT: 1 -MID_SEQ: TCTGATCGAG ---- -REC_TYPE: MID -MID_NUM: 147 -MID_COUNT: 1 -MID_SEQ: TGACATCTCG ---- -REC_TYPE: MID -MID_NUM: 148 -MID_COUNT: 1 -MID_SEQ: TGAGCTAGAG ---- -REC_TYPE: MID -MID_NUM: 149 -MID_COUNT: 1 -MID_SEQ: TGATAGAGCG ---- -REC_TYPE: MID -MID_NUM: 150 -MID_COUNT: 1 -MID_SEQ: TGCGTGTGCG ---- -REC_TYPE: MID -MID_NUM: 151 -MID_COUNT: 1 -MID_SEQ: TGCTAGTCAG ---- -REC_TYPE: MID -MID_NUM: 152 -MID_COUNT: 1 -MID_SEQ: TGTATCACAG ---- -REC_TYPE: MID -MID_NUM: 153 -MID_COUNT: 1 -MID_SEQ: TGTGCGCGTG ---- diff --git a/bp_test/out/read_solexa.out.1 b/bp_test/out/read_solexa.out.1 deleted file mode 100644 index 4d8747c..0000000 --- a/bp_test/out/read_solexa.out.1 +++ /dev/null @@ -1,15 +0,0 @@ -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe -SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434 ---- -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh -SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATAT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373 ---- -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh -SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487 ---- diff --git a/bp_test/out/read_solexa.out.2 b/bp_test/out/read_solexa.out.2 deleted file mode 100644 index a228e53..0000000 --- a/bp_test/out/read_solexa.out.2 +++ /dev/null @@ -1,5 +0,0 @@ -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe -SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434 ---- diff --git a/bp_test/out/read_solexa.out.3 b/bp_test/out/read_solexa.out.3 deleted file mode 100644 index f6edd43..0000000 --- a/bp_test/out/read_solexa.out.3 +++ /dev/null @@ -1,15 +0,0 @@ -SCORES: 40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;11;40;37; -SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434 ---- -SCORES: 40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;39;40;16;40; -SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATAT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373 ---- -SCORES: 40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;27;40;40;40; -SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487 ---- diff --git a/bp_test/out/read_solexa.out.4 b/bp_test/out/read_solexa.out.4 deleted file mode 100644 index d0eb23c..0000000 --- a/bp_test/out/read_solexa.out.4 +++ /dev/null @@ -1,15 +0,0 @@ -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe -SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGtGG -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434 ---- -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh -SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATaT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373 ---- -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh -SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487 ---- diff --git a/bp_test/out/read_solexa.out.5 b/bp_test/out/read_solexa.out.5 deleted file mode 100644 index c389c26..0000000 --- a/bp_test/out/read_solexa.out.5 +++ /dev/null @@ -1,15 +0,0 @@ -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe -SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGtGG -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434 ---- -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh -SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATaT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373 ---- -SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh -SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGaTTT -SEQ_LEN: 36 -SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487 ---- diff --git a/bp_test/out/remove_mids.out.1 b/bp_test/out/remove_mids.out.1 deleted file mode 100644 index c8e8716..0000000 --- a/bp_test/out/remove_mids.out.1 +++ /dev/null @@ -1,32 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: atcgACTCGCGTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: atcgACTCGCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: atcgCTGTACATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: atcgCTGTtCATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- diff --git a/bp_test/out/remove_mids.out.2 b/bp_test/out/remove_mids.out.2 deleted file mode 100644 index 036cdbe..0000000 --- a/bp_test/out/remove_mids.out.2 +++ /dev/null @@ -1,42 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: atcgACTCGCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: atcgCTGTtCATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- diff --git a/bp_test/out/remove_mids.out.3 b/bp_test/out/remove_mids.out.3 deleted file mode 100644 index a791302..0000000 --- a/bp_test/out/remove_mids.out.3 +++ /dev/null @@ -1,52 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 1 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 1 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- diff --git a/bp_test/out/remove_mids.out.4 b/bp_test/out/remove_mids.out.4 deleted file mode 100644 index 9dbc8fd..0000000 --- a/bp_test/out/remove_mids.out.4 +++ /dev/null @@ -1,72 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 1 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 2 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 2 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 1 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 2 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 2 ---- diff --git a/bp_test/out/remove_mids.out.5 b/bp_test/out/remove_mids.out.5 deleted file mode 100644 index ce5d1da..0000000 --- a/bp_test/out/remove_mids.out.5 +++ /dev/null @@ -1,52 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: atcgACTCGCGTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: atcgACTCGCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: atcgACTCaCcTCGTgtgactgact -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 1 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 2 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: gtagtagtagt -SEQ_LEN: 11 -MID: CTGTACATAC -MID_NAME: MID99 -MID_POS: 4 -MID_LEN: 10 -MID_MISMATCHES: 2 ---- diff --git a/bp_test/out/remove_mids.out.6 b/bp_test/out/remove_mids.out.6 deleted file mode 100644 index 7cb712a..0000000 --- a/bp_test/out/remove_mids.out.6 +++ /dev/null @@ -1,52 +0,0 @@ -SEQ_NAME: test_RL12_0_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 0 ---- -SEQ_NAME: test_RL12_1_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 1 ---- -SEQ_NAME: test_RL12_2_mismatches -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 2 ---- -SEQ_NAME: test_RL12_2_mismatches_repeat -SEQ: gtgactgact -SEQ_LEN: 10 -MID: ACTCGCGTCGT -MID_NAME: RL12 -MID_POS: 4 -MID_LEN: 11 -MID_MISMATCHES: 2 ---- -SEQ_NAME: test_GS99_0_mismatches -SEQ: atcgCTGTACATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_1_mismatches -SEQ: atcgCTGTtCATACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- -SEQ_NAME: test_GS99_2_mismatches_repeat -SEQ: atcgCTGTtCAgACgtagtagtagt -SEQ_LEN: 25 ---- diff --git a/bp_test/test/test_find_mids b/bp_test/test/test_find_mids deleted file mode 100755 index f3d30ab..0000000 --- a/bp_test/test/test_find_mids +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -source "$BP_DIR/bp_test/lib/test.sh" - -run "$bp -I $in.1 -p 4 -O $tmp" -assert_no_diff $tmp $out.1 -clean - -run "$bp -I $in.2 -O $tmp" -assert_no_diff $tmp $out.2 -clean diff --git a/bp_test/test/test_read_solexa b/bp_test/test/test_read_solexa deleted file mode 100755 index 5d0a58b..0000000 --- a/bp_test/test/test_read_solexa +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/bash - -source "$BP_DIR/bp_test/lib/test.sh" - -run "$bp -i $in -O $tmp" -assert_no_diff $tmp $out.1 -clean - -run "$bp -i $in -n 1 -O $tmp" -assert_no_diff $tmp $out.2 -clean - -run "$bp -i $in -c -O $tmp" -assert_no_diff $tmp $out.3 -clean - -run "$bp -i $in -s -O $tmp" -assert_no_diff $tmp $out.4 -clean - -run "$bp -i $in -s -C 30 -O $tmp" -assert_no_diff $tmp $out.5 -clean diff --git a/bp_test/test/test_remove_mids b/bp_test/test/test_remove_mids deleted file mode 100755 index 92d0663..0000000 --- a/bp_test/test/test_remove_mids +++ /dev/null @@ -1,27 +0,0 @@ -#!/bin/bash - -source "$BP_DIR/bp_test/lib/test.sh" - -run "$bp -I $in -O $tmp" -assert_no_diff $tmp $out.1 -clean - -run "$bp -I $in -p 4 -O $tmp" -assert_no_diff $tmp $out.2 -clean - -run "$bp -I $in -p 4 -m 1 -O $tmp" -assert_no_diff $tmp $out.3 -clean - -run "$bp -I $in -p 4 -m 2 -O $tmp" -assert_no_diff $tmp $out.4 -clean - -run "$bp -I $in -p 4 -m 2 -g -O $tmp" -assert_no_diff $tmp $out.5 -clean - -run "$bp -I $in -p 4 -m 2 -r -O $tmp" -assert_no_diff $tmp $out.6 -clean