| Next changeset 1:1670f0565000 (2014-06-03) |
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Commit message:
Uploaded tool tarball. |
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added:
pileup_parser.pl pileup_parser.xml test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out test-data/pileup_parser.10col.20-3-yes-yes.pileup.out test-data/pileup_parser.10col.pileup test-data/pileup_parser.6col.20-3-no-no.pileup.out test-data/pileup_parser.6col.20-3-yes-no.pileup.out test-data/pileup_parser.6col.20-3-yes-yes.pileup.out test-data/pileup_parser.6col.40-3-yes-yes.pileup.out test-data/pileup_parser.6col.pileup |
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| diff -r 000000000000 -r ff1ba9b75337 pileup_parser.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pileup_parser.pl Mon Aug 26 15:14:34 2013 -0400 |
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| @@ -0,0 +1,121 @@ +#! /usr/bin/perl -w + +use strict; +use POSIX; + + +die "Usage: pileup_parser.pl <in_file> <ref_base_column> <read_bases_column> <base_quality_column> <coverage column> <qv cutoff> <coverage cutoff> <SNPs only?> <output bed?> <coord_column> <out_file> <total_diff> <print_qual_bases>\n" unless @ARGV == 13; + +my $in_file = $ARGV[0]; +my $ref_base_column = $ARGV[1]-1; # 1 based +my $read_bases_column = $ARGV[2]-1; # 1 based +my $base_quality_column = $ARGV[3]-1; # 1 based +my $cvrg_column = $ARGV[4]-1; # 1 based +my $quality_cutoff = $ARGV[5]; # phred scale integer +my $cvrg_cutoff = $ARGV[6]; # unsigned integer +my $SNPs_only = $ARGV[7]; # set to "Yes" to print only positions with SNPs; set to "No" to pring everything +my $bed = $ARGV[8]; #set to "Yes" to convert coordinates to bed format (0-based start, 1-based end); set to "No" to leave as is +my $coord_column = $ARGV[9]-1; #1 based +my $out_file = $ARGV[10]; +my $total_diff = $ARGV[11]; # set to "Yes" to print total number of deviant based +my $print_qual_bases = $ARGV[12]; #set to "Yes" to print quality and read base columns + +my $invalid_line_counter = 0; +my $first_skipped_line = ""; +my %SNPs = ('A',0,'T',0,'C',0,'G',0); +my $above_qv_bases = 0; +my $SNPs_exist = 0; +my $out_string = ""; +my $diff_count = 0; + +open (IN, "<$in_file") or die "Cannot open $in_file $!\n"; +open (OUT, ">$out_file") or die "Cannot open $out_file $!\n"; + +while (<IN>) { + chop; + next if m/^\#/; + my @fields = split /\t/; + next if $fields[ $ref_base_column ] eq "*"; # skip indel lines + my $read_bases = $fields[ $read_bases_column ]; + die "Coverage column" . ($cvrg_column+1) . " contains non-numeric values. Check your input parameters as well as format of input dataset." if ( not isdigit $fields[ $cvrg_column ] ); + next if $fields[ $cvrg_column ] < $cvrg_cutoff; + my $base_quality = $fields[ $base_quality_column ]; + if ($read_bases =~ m/[\$\^\+-]/) { + $read_bases =~ s/\^.//g; #removing the start of the read segement mark + $read_bases =~ s/\$//g; #removing end of the read segment mark + while ($read_bases =~ m/[\+-]{1}(\d+)/g) { + my $indel_len = $1; + $read_bases =~ s/[\+-]{1}$indel_len.{$indel_len}//; # remove indel info from read base field + } + } + if ( length($read_bases) != length($base_quality) ) { + $first_skipped_line = $. if $first_skipped_line eq ""; + ++$invalid_line_counter; + next; + } + # after removing read block and indel data the length of read_base + # field should identical to the length of base_quality field + + my @bases = split //, $read_bases; + my @qv = split //, $base_quality; + + for my $base ( 0 .. @bases - 1 ) { + if ( ord( $qv[ $base ] ) - 33 >= $quality_cutoff and $bases[ $base ] ne '*') + { + ++$above_qv_bases; + + if ( $bases[ $base ] =~ m/[ATGC]/i ) + { + $SNPs_exist = 1; + $SNPs{ uc( $bases[ $base ] ) } += 1; + $diff_count += 1; + } elsif ( $bases[ $base ] =~ m/[\.,]/ ) { + $SNPs{ uc( $fields[ $ref_base_column ] ) } += 1; + } + } + } + + if ($bed eq "Yes") { + my $start = $fields[ $coord_column ] - 1; + my $end = $fields[ $coord_column ]; + $fields[ $coord_column ] = "$start\t$end"; + } + + if ($print_qual_bases ne "Yes") { + $fields[ $base_quality_column ] = ""; + $fields[ $read_bases_column ] = ""; + } + + + $out_string = join("\t", @fields); # \t$read_bases\t$base_quality"; + foreach my $SNP (sort keys %SNPs) { + $out_string .= "\t$SNPs{$SNP}"; + } + + if ($total_diff eq "Yes") { + $out_string .= "\t$above_qv_bases\t$diff_count\n"; + } else { + $out_string .= "\t$above_qv_bases\n"; + } + + $out_string =~ s/\t+/\t/g; + + if ( $SNPs_only eq "Yes" ) { + print OUT $out_string if $SNPs_exist == 1; + } else { + print OUT $out_string; + } + + + %SNPs = (); + %SNPs = ('A',0,'T',0,'C',0,'G',0); + $above_qv_bases = 0; + $SNPs_exist = 0; + $diff_count = 0; + + +} + +print "Skipped $invalid_line_counter invalid line(s) beginning with line $first_skipped_line\n" if $invalid_line_counter > 0; +close IN; +close OUT; |
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| diff -r 000000000000 -r ff1ba9b75337 pileup_parser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pileup_parser.xml Mon Aug 26 15:14:34 2013 -0400 |
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| b'@@ -0,0 +1,387 @@\n+<tool id="pileup_parser" name="Filter pileup" version="1.0.2">>\n+ <description>on coverage and SNPs</description>\n+ <command interpreter="perl">\n+ #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base\n+ #elif $pileup_type.type_select == "ten" #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base\n+ #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 $diff $qc_base\n+ #end if#\n+ </command>\n+ <inputs>\n+ <param name="input" type="data" format="pileup" label="Select dataset"/>\n+ <conditional name="pileup_type">\n+ <param name="type_select" type="select" label="which contains" help="See "Types of pileup datasets" below for examples">\n+ <option value="six" selected="true">Pileup with six columns (simple)</option>\n+ <option value="ten">Pileup with ten columns (with consensus)</option>\n+ <option value="manual">Set columns manually</option>\n+ </param>\n+ <when value="manual">\n+ <param name="ref_base_column" label="Select column with reference base" type="data_column" numerical="false" data_ref="input" />\n+ <param name="read_bases_column" label="Select column with read bases" type="data_column" numerical="false" data_ref="input" help="something like this: ..,a.."/>\n+ <param name="read_qv_column" label="Select column with base qualities" type="data_column" numerical="false" data_ref="input" help="something like this: IIIGIAI"/>\n+ <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" />\n+ <param name="coord_column" label="Select coordinate column" type="data_column" numerical="true" data_ref="input" />\n+ </when>\n+ <when value="six">\n+ </when>\n+ <when value="ten">\n+ </when>\n+ </conditional>\n+ <param name="qv_cutoff" label="Do not consider read bases with quality lower than" type="integer" value="20" help="No variants with quality below this value will be reported"/>\n+ <param name="cvrg_cutoff" label="Do not report positions with coverage lower than" type="integer" value="3" help="Pileup lines with coverage lower than this value will be skipped"/>\n+ <param name="snps_only" label="Only report variants?" type="select" help="See "Examples 1 and 2" below for explanation">\n+ <option value="No">No</option>\n+ <option value="Yes" selected="true">Yes</option>\n+ </param>\n+ <param name="interval" label="Convert coordinates to intervals?" type="select" help="See "Output format" below for explanation">\n+ <option value="No" selected="true">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <param name="diff" label="Print total number of differences?" type="select" help="See "Example 3" below for explanation">\n+ <option value="No" selected="true">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <param name="qc_base" label="Print quality and base string?" type="select" help="See "Example 4" below for explanation">\n+ <option value="No">No</option>\n+ <option value="Yes" selected="true">Yes</option>\n+ </param>\n+ \n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="out_file1">\n+ <change_format>\n+ <when input="interval" value="Yes" format="interval" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input" value="pileup_parser.6col.pileup"/>\n+ <output name="out_file1" file="pileup_parser.6col.20-3-yes-yes.pil'..b'es to intervals? is set to yes)\n+\n+\n+Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention. \n+ \n+Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines::\n+\n+ chrM 413 G 4 ..t, IIIH 0 0 2 1 3\n+ \n+Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20.\n+\n+-----\n+\n+**Example 1**: Just variants\n+\n+In this mode, the tool only outputs the lines from the input datasets where at least one read contains a sequence variant with quality above the threshold set by the **Do not consider read bases with quality lower than** option. For example, suppose one has a pileup dataset like the following::\n+\n+ chrM 412 A 2 ., II\n+ chrM 413 G 4 ..t, III2\n+ chrM 414 C 4 ..Ta III2\n+ chrM 415 C 4 TTTt III7\n+ \n+To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:\n+\n+.. image:: ${static_path}/images/pileup_parser_help1.png \n+\n+Running the tool with these parameters will return::\n+\n+ chrM 413 G 4 ..t, IIIH 0 0 0 1 3\n+ chrM 414 C 4 ..Ta III2 0 2 0 1 3\n+ chrM 415 C 4 TTTt III7 0 0 0 4 4\n+ \n+**Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord(\'2\')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter.\n+\n+-----\n+\n+**Example 2**: Report everything\n+\n+In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:\n+\n+.. image:: ${static_path}/images/pileup_parser_help2.png \n+\n+will report everything from the original file::\n+\n+ chrM 412 A 2 ., II 2 0 0 0 2\n+ chrM 413 G 4 ..t, III2 0 0 2 1 3\n+ chrM 414 C 4 ..Ta III2 0 2 0 1 3\n+ chrM 415 C 4 TTTt III7 0 0 0 4 4\n+ \n+Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).\n+\n+One can use the last column of this dataset to filter out (using Galaxy\'s **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold.\n+\n+------\n+\n+**Example 3**: Report everything and print total number of differences\n+\n+If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this:\n+\n+.. image:: ${static_path}/images/pileup_parser_help3.png\n+\n+will produce this::\n+\n+ chrM 412 A 2 ., II 2 0 0 0 2 0\n+ chrM 413 G 4 ..t, III2 0 0 2 1 3 1\n+ chrM 414 C 4 ..Ta III2 0 2 0 1 3 1\n+ chrM 415 C 4 TTTt III7 0 0 0 4 4 0\n+ \n+ \n+-----\n+\n+**Example 4**: Report everything, print total number of differences, and ignore qualities and read bases\n+\n+Setting **Print quality and base string?** to **Yes** as shown here:\n+\n+.. image:: ${static_path}/images/pileup_parser_help4.png\n+\n+will produce this::\n+\n+ chrM 412 A 2 2 0 0 0 2 0\n+ chrM 413 G 4 0 0 2 1 3 1\n+ chrM 414 C 4 0 2 0 1 3 1\n+ chrM 415 C 4 0 0 0 4 4 0\n+\n+\n+\n+ \n+</help>\n+</tool>\n' |
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| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
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| @@ -0,0 +1,86 @@ +chrM 13 14 A A 56 0 25 18 16 0 1 0 17 1 +chrM 18 19 T T 55 0 25 20 0 0 1 18 19 1 +chrM 35 36 A A 103 0 25 30 27 0 1 0 28 1 +chrM 58 59 A A 50 0 24 16 12 1 0 0 13 1 +chrM 59 60 C C 50 0 24 16 1 15 0 0 16 1 +chrM 157 158 A G 117 117 19 62 0 0 56 0 56 56 +chrM 170 171 T T 141 0 21 46 0 0 1 45 46 1 +chrM 172 173 A A 130 0 20 42 36 1 0 0 37 1 +chrM 173 174 A A 122 0 21 40 38 1 0 0 39 1 +chrM 187 188 A A 36 0 21 13 11 0 1 0 12 1 +chrM 195 196 T T 17 0 19 5 0 0 1 4 5 1 +chrM 284 285 G G 34 0 15 11 0 0 10 1 11 1 +chrM 285 286 T T 33 0 15 11 1 0 0 7 8 1 +chrM 303 304 G G 41 0 18 13 1 0 11 0 12 1 +chrM 310 311 T T 41 0 18 13 0 1 0 11 12 1 +chrM 347 348 T T 4 0 20 3 1 0 0 2 3 1 +chrM 354 355 A C 14 36 25 4 1 3 0 0 4 3 +chrM 355 356 T C 39 39 25 4 0 4 0 0 4 4 +chrM 380 381 C T 77 108 25 28 0 0 0 24 24 24 +chrM 383 384 A A 76 0 25 30 25 1 0 0 26 1 +chrM 385 386 A G 88 120 25 32 0 0 29 0 29 29 +chrM 414 415 C T 75 75 25 16 0 0 0 15 15 15 +chrM 464 465 C C 169 0 25 65 1 58 0 0 59 1 +chrM 468 469 T T 207 0 25 66 0 0 1 56 57 1 +chrM 471 472 C C 187 0 25 72 1 64 0 0 65 1 +chrM 490 491 C C 212 0 23 79 0 73 0 1 74 1 +chrM 506 507 A A 150 0 21 76 64 1 0 0 65 1 +chrM 510 511 C C 213 0 21 72 1 68 0 0 69 1 +chrM 526 527 A A 164 0 22 58 51 1 0 0 52 1 +chrM 527 528 A A 164 0 22 58 48 0 1 0 49 1 +chrM 536 537 A A 138 0 23 49 42 1 0 0 43 1 +chrM 557 558 T T 83 0 23 27 0 0 1 23 24 1 +chrM 606 607 G G 105 0 24 43 0 0 33 2 35 2 +chrM 618 619 T T 117 0 24 48 0 1 0 34 35 1 +chrM 627 628 G G 108 0 22 57 1 0 51 0 52 1 +chrM 659 660 C C 166 0 19 58 1 53 0 0 54 1 +chrM 668 669 C C 135 0 19 42 1 40 1 0 42 2 +chrM 713 714 A A 127 0 23 96 90 1 0 0 91 1 +chrM 719 720 T T 130 0 24 96 0 0 1 77 78 1 +chrM 736 737 A A 98 0 24 98 87 1 0 0 88 1 +chrM 747 748 A A 97 0 25 86 80 1 0 0 81 1 +chrM 749 750 A A 93 0 25 77 71 2 0 0 73 2 +chrM 759 760 T T 106 0 25 86 0 0 1 69 70 1 +chrM 762 763 A A 99 0 25 83 76 1 0 0 77 1 +chrM 763 764 G G 107 0 25 86 1 0 75 0 76 1 +chrM 764 765 G G 88 0 25 77 0 0 68 1 69 1 +chrM 767 768 T T 102 0 25 71 1 0 0 65 66 1 +chrM 777 778 G G 108 0 25 63 0 0 58 1 59 1 +chrM 784 785 A A 99 0 25 63 51 1 0 0 52 1 +chrM 790 791 G G 155 0 25 60 0 0 55 1 56 1 +chrM 794 795 T T 212 0 25 74 1 0 0 62 63 1 +chrM 807 808 C C 226 0 22 132 1 110 0 0 111 1 +chrM 808 809 T T 242 0 22 134 0 1 0 109 110 1 +chrM 809 810 A A 243 0 22 144 128 0 1 0 129 1 +chrM 814 815 C C 246 0 22 160 1 142 0 0 143 1 +chrM 815 816 A A 255 0 22 169 159 0 1 0 160 1 +chrM 816 817 A A 254 0 22 171 150 1 0 0 151 1 +chrM 819 820 A A 255 0 22 183 157 0 0 1 158 1 +chrM 822 823 T T 252 0 22 192 0 1 0 171 172 1 +chrM 825 826 A A 255 0 22 198 177 0 1 0 178 1 +chrM 829 830 G G 255 0 22 198 1 0 185 0 186 1 +chrM 837 838 G G 255 0 22 169 0 0 160 1 161 1 +chrM 841 842 C C 239 0 22 173 1 156 0 0 157 1 +chrM 856 857 C C 254 0 23 124 1 114 0 0 115 1 +chrM 858 859 A A 250 0 23 118 110 0 1 0 111 1 +chrM 859 860 A A 255 0 23 115 101 1 0 0 102 1 +chrM 864 865 G G 255 0 23 115 1 0 109 0 110 1 +chrM 866 867 A A 224 0 23 105 81 1 0 0 82 1 +chrM 872 873 C C 206 0 23 94 1 84 0 0 85 1 +chrM 873 874 A A 208 0 23 94 80 1 0 0 81 1 +chrM 931 932 C C 53 0 23 22 2 18 0 0 20 2 +chrM 936 937 C C 98 0 24 31 1 21 0 0 22 1 +chrM 950 951 C C 191 0 23 76 1 61 0 0 62 1 +chrM 951 952 A A 223 0 24 81 78 2 0 0 80 2 +chrM 952 953 C C 179 0 24 86 2 67 0 0 69 2 +chrM 956 957 T T 237 0 23 110 0 0 1 91 92 1 +chrM 957 958 C C 251 0 23 117 1 96 0 0 97 1 +chrM 966 967 A A 246 0 23 125 119 1 0 0 120 1 +chrM 974 975 C C 255 0 23 125 1 111 1 0 113 2 +chrM 980 981 C C 247 0 23 123 0 111 1 0 112 1 +chrM 981 982 C C 255 0 23 122 2 106 0 0 108 2 +chrM 982 983 C C 252 0 23 122 1 105 0 0 106 1 +chrM 983 984 A A 250 0 23 119 105 1 0 0 106 1 +chrM 987 988 A A 243 0 23 94 79 1 0 0 80 1 +chrM 1005 1006 C C 138 0 18 49 1 43 0 0 44 1 +chrM 1025 1026 G G 19 0 8 33 0 0 31 1 32 1 |
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| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
| b |
| b'@@ -0,0 +1,86 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|
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.20-3-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.10col.20-3-yes-yes.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
| b |
| b'@@ -0,0 +1,86 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|
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.10col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.10col.pileup Mon Aug 26 15:14:34 2013 -0400 |
| b |
| b'@@ -0,0 +1,1000 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|
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.20-3-no-no.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.20-3-no-no.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
| b |
| b'@@ -0,0 +1,588 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t0\t3\t3\n+chrM\t1054\tA\t3\t..,\tIII\t3\t0\t0\t0\t3\n+chrM\t1055\tG\t3\t..,\t:II\t0\t0\t3\t0\t3\n+chrM\t1056\tC\t3\t..a\tHI%\t0\t2\t0\t0\t2\n+chrM\t1057\tT\t3\t..,\tIII\t0\t0\t0\t3\t3\n+chrM\t1058\tT\t3\t..,\tIII\t0\t0\t0\t3\t3\n+chrM\t1059\tA\t3\t..,\tBII\t3\t0\t0\t0\t3\n+chrM\t1060\tA\t3\t..,\tGII\t3\t0\t0\t0\t3\n+chrM\t1061\tA\t3\t..,\tHII\t3\t0\t0\t0\t3\n+chrM\t1062\tC\t3\t..,\tIII\t0\t3\t0\t0\t3\n+chrM\t1063\tA\t3\t..,\tDII\t3\t0\t0\t0\t3\n+chrM\t1064\tA\t3\t..,\tBII\t3\t0\t0\t0\t3\n+chrM\t1065\tA\t3\t..,\t1II\t2\t0\t0\t0\t2\n+chrM\t1066\tG\t3\t.$.,\t&II\t0\t0\t2\t0\t2\n' |
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.20-3-yes-no.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.20-3-yes-no.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
| b |
| @@ -0,0 +1,2 @@ +chrM 270 C 4 a... ;III 1 3 0 0 4 +chrM 415 C 4 TTTt III7 0 0 0 4 4 |
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.20-3-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.20-3-yes-yes.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
| b |
| @@ -0,0 +1,2 @@ +chrM 269 270 C 4 a... ;III 1 3 0 0 4 +chrM 414 415 C 4 TTTt III7 0 0 0 4 4 |
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.40-3-yes-yes.pileup.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.40-3-yes-yes.pileup.out Mon Aug 26 15:14:34 2013 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chrM 414 415 C 4 TTTt III7 0 0 0 3 3 |
| b |
| diff -r 000000000000 -r ff1ba9b75337 test-data/pileup_parser.6col.pileup --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pileup_parser.6col.pileup Mon Aug 26 15:14:34 2013 -0400 |
| b |
| b'@@ -0,0 +1,1000 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.\tII/II\n+chrM\t262\tG\t5\t,,,..\tII5II\n+chrM\t263\tC\t5\t,,a..\tII%II\n+chrM\t264\tT\t5\t,$,$,..'..b'\t,.,,\tIIII\n+chrM\t915\tA\t4\t,.,,\tIIII\n+chrM\t916\tG\t4\t,.,,\tIII5\n+chrM\t917\tC\t4\t,.,,\tIII5\n+chrM\t918\tG\t4\t,.,,\tIIII\n+chrM\t919\tC\t4\t,.,,\tIII<\n+chrM\t920\tG\t4\t,.,,\tIIII\n+chrM\t921\tC\t4\t,.,,\tIIII\n+chrM\t922\tA\t4\t,.,,\tIIII\n+chrM\t923\tC\t4\t,.,,\tIII8\n+chrM\t924\tA\t4\t,.,,\tIFII\n+chrM\t925\tC\t4\t,.,,\tIIII\n+chrM\t926\tA\t4\t,.,,\tIIII\n+chrM\t927\tC\t4\t,.,,\tIIII\n+chrM\t928\tC\t5\t,.,,^:,\tIIII:\n+chrM\t929\tG\t5\t,.,,,\tIIIE:\n+chrM\t930\tC\t5\t,.,,,\tIIIII\n+chrM\t931\tC\t5\t,.,,,\tIIIIF\n+chrM\t932\tC\t5\t,.,,,\tIIIIC\n+chrM\t933\tG\t5\t,$.,,,\tI?II:\n+chrM\t934\tT\t4\t.$,,,\t4II>\n+chrM\t935\tC\t3\t,,,\tIII\n+chrM\t936\tA\t3\t,,,\tIII\n+chrM\t937\tC\t3\t,,,\tII1\n+chrM\t938\tC\t3\t,,,\tIII\n+chrM\t939\tC\t3\t,,,\tIII\n+chrM\t940\tT\t3\t,$,,\tIII\n+chrM\t941\tC\t2\t,,\tII\n+chrM\t942\tC\t2\t,,\tI\'\n+chrM\t943\tT\t2\t,,\tII\n+chrM\t944\tT\t2\t,,\tII\n+chrM\t945\tA\t2\t,,\tII\n+chrM\t946\tA\t2\t,$,\tII\n+chrM\t947\tA\t1\t,\tI\n+chrM\t948\tT\t1\t,\tI\n+chrM\t949\tA\t1\t,\tI\n+chrM\t950\tT\t1\t,\tI\n+chrM\t951\tC\t1\t,\tI\n+chrM\t952\tA\t1\t,\tI\n+chrM\t953\tC\t1\t,\tI\n+chrM\t954\tA\t1\t,\tI\n+chrM\t955\tA\t2\t,^:.\tII\n+chrM\t956\tA\t2\t,.\tII\n+chrM\t957\tT\t2\t,.\tII\n+chrM\t958\tC\t3\t,.^:.\tIII\n+chrM\t959\tA\t3\t,..\tIII\n+chrM\t960\tT\t3\t,..\tIII\n+chrM\t961\tA\t3\t,..\tIII\n+chrM\t962\tA\t3\t,..\tIII\n+chrM\t963\tC\t4\t,$..^:.\tIIII\n+chrM\t964\tA\t3\t...\tI(;\n+chrM\t965\tT\t3\t...\tIII\n+chrM\t966\tA\t4\t...^:.\tIIII\n+chrM\t967\tA\t4\t....\tIIII\n+chrM\t968\tC\t4\t....\tIEII\n+chrM\t969\tA\t4\t....\tIIII\n+chrM\t970\tT\t4\t....\tIIII\n+chrM\t971\tA\t4\t....\tIIII\n+chrM\t972\tA\t4\t....\tIIII\n+chrM\t973\tA\t4\t....\tII0I\n+chrM\t974\tA\t5\t....^:.\tIIIII\n+chrM\t975\tC\t5\t.....\tIIIII\n+chrM\t976\tC\t5\t.....\tIIIII\n+chrM\t977\tG\t5\t.....\tIIIII\n+chrM\t978\tT\t5\t.....\tIIIII\n+chrM\t979\tG\t5\t.....\tI0III\n+chrM\t980\tA\t5\t.....\tIIII4\n+chrM\t981\tC\t5\t.....\tIIIII\n+chrM\t982\tC\t5\t.....\tIIIII\n+chrM\t983\tC\t5\t.....\tIIIII\n+chrM\t984\tA\t5\t.....\t-IGII\n+chrM\t985\tA\t5\t.....\t4GIII\n+chrM\t986\tA\t5\t.....\tBDGII\n+chrM\t987\tC\t5\t.....\tIDIII\n+chrM\t988\tA\t5\t.....\t@<III\n+chrM\t989\tT\t5\t.....\tIIIII\n+chrM\t990\tA\t5\t.$....\tI@III\n+chrM\t991\tT\t4\t....\tIICI\n+chrM\t992\tG\t4\tT...\t)III\n+chrM\t993\tA\t4\t.$...\t?ICI\n+chrM\t994\tA\t3\t...\tIII\n+chrM\t995\tA\t3\t...\tIII\n+chrM\t996\tG\t3\t...\tIII\n+chrM\t997\tG\t3\t...\tIII\n+chrM\t998\tA\t3\t.$..\t4II\n+chrM\t999\tG\t3\t..^:.\tIII\n+chrM\t1000\tA\t3\t...\tIII\n+chrM\t1001\tC\t3\t.$..\tIII\n+chrM\t1002\tA\t2\t..\tII\n+chrM\t1003\tA\t2\t..\tII\n+chrM\t1004\tG\t2\t..\tII\n+chrM\t1005\tT\t2\t..\tII\n+chrM\t1006\tC\t2\t..\tII\n+chrM\t1007\tG\t2\t..\tCI\n+chrM\t1008\tT\t2\t..\tII\n+chrM\t1009\tA\t2\t.$.\tII\n+chrM\t1010\tA\t1\t.\tI\n+chrM\t1011\tC\t1\t.\tI\n+chrM\t1012\tA\t1\t.\tI\n+chrM\t1013\tA\t1\t.\tI\n+chrM\t1014\tG\t1\t.\tI\n+chrM\t1015\tG\t1\t.\tI\n+chrM\t1016\tT\t1\t.\tI\n+chrM\t1017\tA\t1\t.\tI\n+chrM\t1018\tA\t1\t.\tI\n+chrM\t1019\tG\t1\t.\tI\n+chrM\t1020\tT\t1\t.\tI\n+chrM\t1021\tA\t1\t.\tI\n+chrM\t1022\tT\t1\t.\tI\n+chrM\t1023\tA\t1\t.\tI\n+chrM\t1024\tC\t1\t.\tI\n+chrM\t1025\tC\t1\t.\tI\n+chrM\t1026\tG\t1\t.\tI\n+chrM\t1027\tG\t1\t.\tI\n+chrM\t1028\tA\t1\t.\tI\n+chrM\t1029\tA\t1\t.\tI\n+chrM\t1030\tG\t1\t.\tI\n+chrM\t1031\tG\t2\t.^:.\tII\n+chrM\t1032\tT\t2\t..\tEI\n+chrM\t1033\tG\t2\t..\tII\n+chrM\t1034\tT\t2\t.$.\tII\n+chrM\t1035\tA\t2\t.^:.\tII\n+chrM\t1036\tC\t2\t..\tII\n+chrM\t1037\tT\t2\t..\tII\n+chrM\t1038\tT\t2\t..\tII\n+chrM\t1039\tG\t2\t..\tII\n+chrM\t1040\tG\t2\t..\tII\n+chrM\t1041\tA\t2\t..\tII\n+chrM\t1042\tT\t2\t..\tII\n+chrM\t1043\tA\t3\t..^:,\tIII\n+chrM\t1044\tA\t3\t..,\tIII\n+chrM\t1045\tC\t3\t..,\tII7\n+chrM\t1046\tC\t3\t..,\tII-\n+chrM\t1047\tA\t3\t..,\tIII\n+chrM\t1048\tA\t3\t..,\tIII\n+chrM\t1049\tA\t3\t..,\tIII\n+chrM\t1050\tG\t3\t..,\tIII\n+chrM\t1051\tT\t3\t..,\tIII\n+chrM\t1052\tG\t3\t..,\tIII\n+chrM\t1053\tT\t3\t..,\tGII\n+chrM\t1054\tA\t3\t..,\tIII\n+chrM\t1055\tG\t3\t..,\t:II\n+chrM\t1056\tC\t3\t..a\tHI%\n+chrM\t1057\tT\t3\t..,\tIII\n+chrM\t1058\tT\t3\t..,\tIII\n+chrM\t1059\tA\t3\t..,\tBII\n+chrM\t1060\tA\t3\t..,\tGII\n+chrM\t1061\tA\t3\t..,\tHII\n+chrM\t1062\tC\t3\t..,\tIII\n+chrM\t1063\tA\t3\t..,\tDII\n+chrM\t1064\tA\t3\t..,\tBII\n+chrM\t1065\tA\t3\t..,\t1II\n+chrM\t1066\tG\t3\t.$.,\t&II\n+chrM\t1067\tC\t2\t.,\tII\n+chrM\t1068\tA\t2\t.,\tII\n+chrM\t1069\tT\t2\t.,\tII\n+chrM\t1070\tC\t2\t.$,\tII\n+chrM\t1071\tC\t1\t,\tI\n+chrM\t1072\tA\t1\t,\tI\n+chrM\t1073\tG\t1\t,\tI\n+chrM\t1074\tC\t1\t,\tI\n+chrM\t1075\tT\t1\t,\tI\n+chrM\t1076\tT\t1\t,\tI\n+chrM\t1077\tA\t1\t,\tI\n+chrM\t1078\tC\t1\t,$\tI\n+chrM\t1090\tT\t1\t^:,\tI\n+chrM\t1091\tT\t1\t,\tI\n+chrM\t1092\tC\t1\tn\t"\n+chrM\t1093\tA\t1\t,\tI\n+chrM\t1094\tC\t1\t,\tI\n+chrM\t1095\tT\t1\t,\t7\n+chrM\t1096\tC\t1\ta\tB\n+chrM\t1097\tA\t1\t,\tI\n+chrM\t1098\tA\t1\t,\tI\n+chrM\t1099\tA\t1\t,\tI\n+chrM\t1100\tA\t1\t,\tI\n+chrM\t1101\tT\t1\t,\tI\n+chrM\t1102\tG\t2\t,^:,\t(I\n+chrM\t1103\tA\t2\t,,\tII\n+chrM\t1104\tA\t2\t,,\tI+\n+chrM\t1105\tC\t2\t,,\t.I\n+chrM\t1106\tA\t2\t,,\t8I\n' |