Mercurial > repos > artbio > concatenate_multiple_datasets
changeset 0:122dbfdf0826 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/concat_multi_datasets commit 75811bd85c9d175d9bc7b2c4fd723adc3a361f0f
| author | artbio |
|---|---|
| date | Tue, 09 Jul 2019 09:51:52 -0400 |
| parents | |
| children | |
| files | catWrapper.xml test-data/1.bed test-data/1.fastq.gz test-data/1_f.fastq test-data/1_f.fastq.gz test-data/1_options.fastq.gz test-data/1_r.fastq test-data/1_r.fastq.gz test-data/2.bed test-data/2.fastq test-data/2_f.fastq test-data/2_r.fastq test-data/3.fastq test-data/3_f.fastq test-data/3_r.fastq test-data/4.fastq test-data/4_f.fastq test-data/4_r.fastq test-data/cat_wrapper_out1.bed test-data/cat_wrapper_out2.bed test-data/cat_wrapper_out3.bed test-data/f.fastq test-data/r.fastq |
| diffstat | 23 files changed, 1447 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/catWrapper.xml Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,675 @@ +<tool id="cat_multi_datasets" name="Concatenate multiple datasets" version="1.4.1"> + <description>tail-to-head by specifying how</description> + <command><![CDATA[ + #if $headers == 0: + #set $concat_command = "cat" + #else: + #set $concat_command = 'tail -q -n +'+ str(int($headers)+1) + #end if + printf "Concatenating files:\n" && + #if $global_condition.input_type == "singles": + #if $dataset_names == "No": + #for $file in $global_condition.inputs + printf "${file.element_identifier}..." && + #if $file.ext: + #if $file.ext[-2:] == "gz" and $headers != 0: + gzip -dc '$file' | $concat_command | gzip -c >> '$out_file1' && + #else: + $concat_command '$file' >> '$out_file1' && + #end if + #else: + $concat_command '$file' >> '$out_file1' && + #end if + printf "Done\n" && + #end for + sleep 1 + #else: + #for $file in $global_condition.inputs + printf "${file.element_identifier}..." && + #if $file.ext[-2:] == "gz" and $headers != 0: + printf "# ${file.element_identifier}\n" | gzip -c >> '$out_file1' && + gzip -dc "$file" | $concat_command |gzip -c >> '$out_file1' && + #else: + printf "# ${file.element_identifier}\n" >> '$out_file1' && + $concat_command "$file" >> '$out_file1' && + #end if + printf "Done\n" && + #end for + sleep 1 + #end if + #else if $global_condition.input_type == "simple_collections": + mkdir concatenated && + #if $dataset_names == "No": + #for $x, $y in zip($global_condition.input_1, $global_condition.input_2): + printf "${x.element_identifier} and ${y.element_identifier}..." && + #if $x.ext[-2:] == "gz" and $headers != 0: + gzip -dc '$x' | $concat_command | gzip -c > concatenated/'${x.element_identifier}.listed.${x.ext}.listed' && + gzip -dc '$y' | $concat_command | gzip -c >> concatenated/'${x.element_identifier}.listed.${x.ext}.listed' && + #else: + $concat_command '$x' '$y' > concatenated/'${x.element_identifier}.listed.${x.ext}.listed' && + #end if + printf "Done\n" && + #end for + sleep 1 + #else: + #for $x, $y in zip($global_condition.input_1, $global_condition.input_2) + printf "${x.element_identifier} and ${y.element_identifier}..." && + #if $x.ext[-2:] == "gz" and $headers != 0: + printf "# ${x.element_identifier}\n" | gzip -c > concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + gzip -dc '$x' | $concat_command | gzip -c >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + printf "# ${y.element_identifier}\n" | gzip -c >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + gzip -dc '$y' | $concat_command | gzip -c >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + #else: + printf "# ${x.element_identifier}\n" > concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + $concat_command '$x'>> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + printf "# ${y.element_identifier}\n" >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + $concat_command '$y' >> concatenated/'${x.element_identifier}_${y.element_identifier}.listed.${x.ext}.listed' && + #end if + printf "Done\n" && + #end for + sleep 1 + #end if + #else if $global_condition.input_type == "paired_collection": + #if $global_condition.paired_cat_type == "by_strand": + mkdir concatenated && + #if $dataset_names == "No": + #for $file in $global_condition.inputs + printf "${file.element_identifier}- forward and reverse..." && + #if $file['forward'].ext[-2:] == "gz" and $headers != 0: + gzip -dc $file['forward'] | $concat_command | gzip -c >> concatenated/forward.listed.${file['forward'].ext}.listed && + gzip -dc $file['reverse'] | $concat_command | gzip -c >> concatenated/reverse.listed.${file['reverse'].ext}.listed && + #else: + $concat_command $file['forward'] >> concatenated/forward.listed.${file['forward'].ext}.listed && + $concat_command $file['reverse'] >> concatenated/reverse.listed.${file['reverse'].ext}.listed && + #end if + printf "Done\n" && + #end for + sleep 1 + #else: + #for $file in $global_condition.inputs.keys(): + printf "$file - forward and reverse..." && + #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0: + printf "# ${file}_forward\n" | gzip -c >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed && + gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed && + printf "# ${file}_reverse\n" | gzip -c >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed && + gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed && + #else: + printf "# ${file}_forward\n" >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed && + $concat_command $global_condition.inputs[$file]['forward'] >> concatenated/forward.listed.${global_condition.inputs[$file]['forward'].ext}.listed && + printf "# ${file}_reverse\n" >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed && + $concat_command $global_condition.inputs[$file]['reverse'] >> concatenated/reverse.listed.${global_condition.inputs[$file]['reverse'].ext}.listed && + #end if + printf "Done\n" && + #end for + sleep 1 + #end if + #else if $global_condition.paired_cat_type == "by_pair": + mkdir concatenated && + #if $dataset_names == "No": + #for $file in $global_condition.inputs.keys(): + printf "$file - forward and reverse..." && + #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0: + gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c + > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c + >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + #else: + $concat_command $global_condition.inputs[$file]['forward'] + > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + $concat_command $global_condition.inputs[$file]['reverse'] + >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + #end if + printf "Done\n" && + #end for + sleep 1 + #else: + #for $file in $global_condition.inputs.keys(): + printf "$file - forward and reverse..." && + #if $global_condition.inputs[$file]['reverse'].ext[-2:] == "gz" and $headers != 0: + printf "# ${file}_forward\n" | gzip -c > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c + >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + printf "# ${file}_reverse\n" | gzip -c >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c + >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + #else: + printf "# ${file}_forward\n" > concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + $concat_command $global_condition.inputs[$file]['forward'] + >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + printf "# ${file}_reverse\n" >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + $concat_command $global_condition.inputs[$file]['reverse'] + >> concatenated/'${file}.listed.${global_condition.inputs[$file]['reverse'].ext}.listed' && + #end if + printf "Done\n" && + #end for + sleep 1 + #end if + #else if $global_condition.paired_cat_type == "all": + mkdir concatenated && + #set $base_name=$global_condition.inputs.element_identifier + #set $extention=$global_condition.inputs[$global_condition.inputs.keys()[0]]['forward'].ext + #if $dataset_names == "No": + #for $file in $global_condition.inputs.keys(): + printf "$file - forward and reverse..." && + #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0: + gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c >> c'$paired_out_file' && + gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c >> '$paired_out_file' && + #else: + $concat_command + $global_condition.inputs[$file]['forward'] + >> '$paired_out_file' && + $concat_command + $global_condition.inputs[$file]['reverse'] + >> '$paired_out_file' && + #end if + printf "Done\n" && + #end for + sleep 1 + #else: + #for $file in $global_condition.inputs.keys(): + printf "$file - forward and reverse..." && + #if $global_condition.inputs[$file]['forward'].ext[-2:] == "gz" and $headers != 0: + printf "# ${file}_forward\n" | gzip -c > '$paired_out_file' && + gzip -dc $global_condition.inputs[$file]['forward'] | $concat_command | gzip -c >> '$paired_out_file' && + printf "# ${file}_reverse\n" | gzip -c >> '$paired_out_file' && + gzip -dc $global_condition.inputs[$file]['reverse'] | $concat_command | gzip -c >> '$paired_out_file' && + #else: + printf "# ${file}_forward\n" > '$paired_out_file' && + $concat_command + $global_condition.inputs[$file]['forward'] + >> '$paired_out_file' && + printf "# ${file}_reverse\n" >> '$paired_out_file' && + $concat_command + $global_condition.inputs[$file]['reverse'] + >> '$paired_out_file' && + #end if + printf "Done\n" && + #end for + sleep 1 + #end if + #end if + #else if $global_condition.input_type == "nested_collection": + mkdir concatenated && + #if $dataset_names == "No": + #for $sub_list in $global_condition.inputs: + #set $file_base_name=$sub_list.element_identifier + #for $sub_list_element in $sub_list: + printf "${file_base_name} - ${sub_list_element.element_identifier}..." && + #if $sub_list_element.ext[-2:] == "gz" and $headers != 0: + gzip -dc ${sub_list_element} | $concat_command | gzip -c >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' && + #else: + $concat_command ${sub_list_element} >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' && + #end if + printf "Done\n" && + #end for + #end for + sleep 1 + #else: + #for $sub_list in $global_condition.inputs: + #set $file_base_name=$sub_list.element_identifier + #for $sub_list_element in $sub_list: + printf "${file_base_name} - ${sub_list_element.element_identifier}..." && + #if $sub_list_element.ext[-2:] == "gz" and $headers != 0: + printf "# ${sub_list_element.element_identifier}\n" | gzip -c >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' && + gzip -dc ${sub_list_element} | $concat_command | gzip -c >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' && + #else: + printf "# ${sub_list_element.element_identifier}\n" >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' && + $concat_command ${sub_list_element} >> concatenated/'${file_base_name}.listed.${sub_list_element.ext}.listed' && + #end if + printf "Done\n" && + #end for + #end for + sleep 1 + #end if + #end if + ]]> + </command> + <inputs> + <conditional name="global_condition"> + <param name="input_type" type="select" label="What type of data do you wish to concatenate?" help="Depending on the type of input selected the concatenation options will differ"> + <option value="singles">Single datasets</option> + <option value="simple_collections">2 Collections</option> + <option value="paired_collection">Paired collection</option> + <option value="nested_collection">Nested collection</option> + </param> + <when value="singles"> + <param name="inputs" type="data" label="Concatenate Datasets" multiple="True" help="All inputed datasets will be concatenated tail-to-head."/> + </when> + <when value="paired_collection"> + <param name="inputs" type="data_collection" collection_type="list:paired" label="Input paired collection to concatenate"/> + <param name="paired_cat_type" type="select" label="What type of concatenation do you wish to perform?"> + <option value="by_strand">Concatenate all datsets of same strand (outputs a single pair of datasets)</option> + <option value="by_pair">Concatenate pairs of datasets (outputs an unpaired collection of datasets)</option> + <option value="all">Concatenate all datasets into a single file regardless of strand (outputs a single file)</option> + </param> + </when> + <when value="simple_collections"> + <param name="input_1" type="data_collection" collection_type="list" label="Input first collection" help="The first collection contains the datasets that will be written first in the concatenated file" /> + <param name="input_2" type="data_collection" collection_type="list" label="Input second collection" help="The second collection contains the datasets that will be written last in the concatenated file" /> + </when> + <when value="nested_collection"> + <param name="inputs" type="data_collection" collection_type="list:list" label="Input nested collection" help="The Nested collection which items you want to concatenate." /> + </when> + </conditional> + <param name="dataset_names" type="boolean" label="Include dataset names?" truevalue="Yes" falsevalue="No" checked="false" help="If 'Yes' is selected '#name of dataset' will be added when concatenating."/> + <param name="headers" type="integer" label="Number of lines to skip at the beginning of each concatenation:" value="0" help="This paremeter exists so as to not concatenate comments or headers contained at the start of the files."/> + </inputs> + <outputs> + <data name="out_file1" format_source="inputs" metadata_source="inputs" label="Concatenated datasets"> + <filter>global_condition['input_type'] == 'singles'</filter> + </data> + <data name="paired_out_file" label="${global_condition.inputs.element_identifier}" auto_format="true"> + <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'all'</filter> + </data> + <collection name="paired_output" type="paired" label="Concatenation by strtand"> + <discover_datasets pattern="(?P<name>.*)\.listed\.(?P<ext>.*)\.listed" visible="false" directory="concatenated"/> + <filter>global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_strand'</filter> + </collection> + <collection name="list_output" type="list" label="Concatenation by pairs"> + <discover_datasets pattern="(?P<identifier_0>.*)\.listed\.(?P<ext>.*)\.listed" visible="false" directory="concatenated"/> + <filter>(global_condition['input_type'] == 'paired_collection' and global_condition['paired_cat_type'] == 'by_pair') or (global_condition['input_type'] == 'simple_collections') or (global_condition['input_type'] == 'nested_collection')</filter> + </collection> + </outputs> + <tests> + <!-- Single files concatenation --> + <test> <!-- Test 2 single files concatenation with no other option --> + <param name="input_type" value="singles" /> + <param name="inputs" value="1.bed,2.bed"/> + <param name="dataset_names" value="No" /> + <param name="headers" value="0" /> + <output name="out_file1" file="cat_wrapper_out1.bed"/> + </test> + <test> <!-- Test 2 single files concatenation with dataset names activated --> + <param name="input_type" value="singles" /> + <param name="inputs" value="1.bed,2.bed"/> + <param name="dataset_names" value="Yes" /> + <param name="headers" value="0" /> + <output name="out_file1" file="cat_wrapper_out2.bed"/> + </test> + <test> <!-- Test 2 single files concatenation skipping 1 line --> + <param name="input_type" value="singles" /> + <param name="inputs" value="1.bed,2.bed"/> + <param name="dataset_names" value="No" /> + <param name="headers" value="1" /> + <output name="out_file1" file="cat_wrapper_out3.bed"/> + </test> + <test> <!-- Test gz handling with no options --> + <param name="input_type" value="singles" /> + <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/> + <param name="dataset_names" value="No" /> + <param name="headers" value="0" /> + <output name="out_file1" file="1.fastq.gz" decompress="True"/> + </test> + <test> <!-- Test gz handling with options --> + <param name="input_type" value="singles" /> + <param name="inputs" value="1_f.fastq.gz,1_r.fastq.gz"/> + <param name="dataset_names" value="Yes" /> + <param name="headers" value="4" /> + <output name="out_file1" file="1_options.fastq.gz" decompress="True"/> + </test> + <!-- Test paired options --> + <test> <!-- Test paired collection concatenation by_pair with no other option --> + <param name="input_type" value="paired_collection" /> + <param name="paired_cat_type" value="by_pair"/> + <param name="inputs"> + <collection type="list:paired"> + <element name="2"> + <collection type="paired"> + <element name="forward" value="2_f.fastq"/> + <element name="reverse" value="2_r.fastq"/> + </collection> + </element> + <element name="3"> + <collection type="paired"> + <element name="forward" value="3_f.fastq"/> + <element name="reverse" value="3_r.fastq"/> + </collection> + </element> + <element name="4"> + <collection type="paired"> + <element name="forward" value="4_f.fastq"/> + <element name="reverse" value="4_r.fastq"/> + </collection> + </element> + </collection> + </param> + <param name="dataset_names" value="No" /> + <param name="headers" value="0" /> + <output_collection name="list_output" type="list" > + <element name="2" file="2.fastq"/> + <element name="3" file="3.fastq"/> + <element name="4" file="4.fastq"/> + </output_collection> + </test> + <test> <!-- Test paired collection concatenation by_strand with no other option --> + <param name="input_type" value="paired_collection" /> + <param name="paired_cat_type" value="by_strand"/> + <param name="inputs"> + <collection type="list:paired"> + <element name="2"> + <collection type="paired"> + <element name="forward" value="2_f.fastq"/> + <element name="reverse" value="2_r.fastq"/> + </collection> + </element> + <element name="3"> + <collection type="paired"> + <element name="forward" value="3_f.fastq"/> + <element name="reverse" value="3_r.fastq"/> + </collection> + </element> + <element name="4"> + <collection type="paired"> + <element name="forward" value="4_f.fastq"/> + <element name="reverse" value="4_r.fastq"/> + </collection> + </element> + </collection> + </param> + <param name="dataset_names" value="No" /> + <param name="headers" value="0" /> + <output_collection name="paired_output" type="paired" > + <element name="forward" file="f.fastq"/> + <element name="reverse" file="r.fastq"/> + </output_collection> + </test> + <test> <!-- Test 2 collections concatenation --> + <param name="input_type" value="simple_collections" /> + <param name="collection_cat_type" value="two_collections"/> + <param name="input_1"> + <collection type="list"> + <element name="2" value="2_f.fastq"/> + <element name="3" value="3_f.fastq"/> + <element name="4" value="4_f.fastq"/> + </collection> + </param> + <param name="input_2"> + <collection type="list"> + <element name="2" value="2_r.fastq"/> + <element name="3" value="3_r.fastq"/> + <element name="4" value="4_r.fastq"/> + </collection> + </param> + <param name="dataset_names" value="No" /> + <param name="headers" value="0" /> + <output_collection name="list_output" type="list" count="3" > + <element name="2" file="2.fastq"/> + <element name="3" file="3.fastq"/> + <element name="4" file="4.fastq"/> + </output_collection> + </test> + <test> <!-- Test 2 collections concatenation with other options--> + <param name="input_type" value="simple_collections" /> + <param name="collection_cat_type" value="two_collections"/> + <param name="input_1"> + <collection type="list"> + <element name="1_f.fastq.gz" value="1_f.fastq.gz"/> + </collection> + </param> + <param name="input_2"> + <collection type="list"> + <element name="1_r.fastq.gz" value="1_r.fastq.gz"/> + </collection> + </param> + <param name="dataset_names" value="Yes" /> + <param name="headers" value="4" /> + <output_collection name="list_output" type="list" count="1" > + <element name="1_f.fastq.gz_1_r.fastq.gz" file="1_options.fastq.gz" decompress="True"/> + </output_collection> + </test> + <test> <!-- Test nested collections concatenation --> + <param name="input_type" value="nested_collection" /> + <param name="inputs"> + <collection type="list:list"> + <element name="2"> + <collection type="list"> + <element name="2_f" value="2_f.fastq" ftype="fastq"/> + <element name="2_r" value="2_r.fastq" ftype="fastq"/> + </collection> + </element> + <element name="3"> + <collection type="list"> + <element name="3" value="3.fastq" ftype="fastq"/> + </collection> + </element> + </collection> + </param> + <param name="dataset_names" value="No" /> + <param name="headers" value="0" /> + <output_collection name="list_output" type="list" count="2" > + <element name="2" file="2.fastq"/> + <element name="3" file="3.fastq"/> + </output_collection> + </test> + <test> <!-- Test nested collections concatenation with options and gzip--> + <param name="input_type" value="nested_collection" /> + <param name="inputs"> + <collection type="list:list"> + <element name="1"> + <collection type="list"> + <element name="1_f.fastq.gz" value="1_f.fastq.gz" ftype="fastq.gz"/> + <element name="1_r.fastq.gz" value="1_r.fastq.gz" ftype="fastq.gz"/> + </collection> + </element> + </collection> + </param> + <param name="dataset_names" value="Yes" /> + <param name="headers" value="4" /> + <output_collection name="list_output" type="list" count="1" > + <element name="1" file="1_options.fastq.gz" decompress="True"/> + </output_collection> + </test> + </tests> + <help> + +.. class:: warningmark + +**WARNINGS:** + +- This tool does not check if the datasets being concatenated are in the same format. +- When concatenating 2 collections make sure the first collection is the one with the most items. +- This tool can't handle nested collection deeper than list:list. + +----- + +**What it does** + +Concatenates datasets and paired collections with multiple options: + + - When the input is a paired collection: + + - concatenation by strand : forward and reverse datasets are concatenated separately and a list with a single forward - reverse dataset pair is returned + + - concatenation by pair : forward - reverse dataset pairs are concatenated and a simple dataset collection is returned + + - whole collection concatenation : all datasets in the collection are concatenated and a single dataset is returned + + - When the inputs are 2 collections: datasets are concatenated in a pairwise combination and a single dataset collection is returned + + - When nested collection concatenation: datasets in each sub-collection are concatenated and a simple dataset collection is returned + + - Skipping lines before concatenation to avoid headers + + - Add the name of the concatenated files as separator + +----- + +**Single datasets concatenation example** + +Concatenating Dataset:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + +with Dataset1:: + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + +and with Dataset2:: + + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + + +will result in the following:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + chr2 100000030 200000955 P 0 + + chr2 100000015 200000999 Q 0 + + +----- + +**2 Collections concatenation** + +1rst collection:: + + a + b + c + d + +2nd collection:: + + 1 + 2 + 3 + 4 + +Concatenation result:: + + A single collection containing: + + a concatenated with 1 + b concatenated with 2 + c concatenated with 3 + d concatenated with 4 + +----- + +**Paired collection concatenation example** + +1rst pair:: + + forward - reverse + +2nd pair:: + + forward - reverse + +- Concatenation by strand:: + + concatenates: + + 1rst forward + 2nd forward + 1rst reverse + 2nd reverse + + outputs: + + 1 pair + +- Concatenation by pair:: + + concatenates: + + 1rst forward + 1rst reverse + 2nd forward + 2nd reverse + + outputs: + + 2 datasets + +- Concatenate all:: + + concatenates: + + 1rst forward + 1rst reverse + 2nd forward + 2nd reverse + + outputs: + + 1 dataset + +----- + +**Nested collection concatenation example** + +Nested collection: + + - Experiment + + - Sample_1 + + - Sample_1_file_1 + - Sample_1_file_2 + + - Sample_2 + + - Sample_2_file_1 + - Sample_2_file_2 + - Sample_2_file_3 + +Concatenation result:: + + A single collection containing: + + - Sample_1: (Sample_1_file_1 + Sample_1_file_2) + - Sample_2: (Sample_2_file_1 + Sample_2_file_2 + Sample_2_file_3) + +----- + +**When selecting "Include dataset names" when concatenating files**: + +1rst file name="first_tabular":: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + +2nd file name="second_tabular":: + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + +output:: + + # first_tabular + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + # second_tabular + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + +----- + +**Skiping lines** + +1rst file:: + + chrX 151087187 151087355 A 0 - + chrX 151572400 151572481 B 0 + + +2nd file:: + + chr1 151242630 151242955 X 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + +skipping 1 line + +output:: + + chrX 151572400 151572481 B 0 + + chr1 151271715 151271999 Y 0 + + chr1 151278832 151279227 Z 0 - + +----- + +Adapted from galaxy's catWrapper.xml to allow multiple input files. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_f.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:18757:1118 1:N:0:GCCAAT +CACCGTTACATCACACCAACCAAGATTACATCACACCACTCAGGATGACAGACAGTAATCCTGTTTGTTATATANG ++ +AAAAAEEEEEEEEEEEEAEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEE<EEEEEEEEE#A +@NS500801:189:HWGFJBGX5:1:11101:21956:1118 1:N:0:GCCAAT +CTTACAACCAACTTGATATCACATTCAGCCTGAGGATTTGTTGCTTCATCTTCAGTTCTGTAACATTAAATGGANT ++ +AAAAAAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEEEEEEEE#E +@NS500801:189:HWGFJBGX5:1:11101:17695:1118 1:N:0:GCCAAT +GGGTAATTGATCATCTGTCATGCCAACAGCAAGCAAGGTCTTCCCAGTGCAGCAACAACGTTCAGAATGGATACNG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEE/AEE/EEEEEEAEEEEE#E
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_r.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:18757:1118 2:N:0:GCCAAT +CCAAAATCTGNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGAGAAGCTGCAGCTCGAGNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEEEEEEEEE<E############### +@NS500801:189:HWGFJBGX5:1:11101:21956:1118 2:N:0:GCCAAT +ATTTAAGATTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGCTTTGGGAGGATTATTTTNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEEEEEEEEEEE############### +@NS500801:189:HWGFJBGX5:1:11101:17695:1118 2:N:0:GCCAAT +AACTTGCATGNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNACGTTGTTGCTGCACTGGGANNNNNNNNNNNNNNN ++ +AAAAAEEAEE#EE############################EAEEEEEEEEEEAAEEEEEE###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.bed Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,68 @@ +chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + +chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,24 @@ +@NS500801:189:HWGFJBGX5:1:11101:3766:1118 1:N:0:ACAGTG +ATCCCATACTGCTCAAAATAATCTCGTAGGTGATGTTCTTCAGTGTCTTCTTTAATACCACCAACAAAGATCTTNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE#E +@NS500801:189:HWGFJBGX5:1:11101:25700:1118 1:N:0:ACAGTG +GTGCCGTTGAATTTGCCGTGAGTGGAGTCATACTGGAACATGTAGACCATGTAGTTGAGGTCAATGAAGGGGTCNT ++ +AAAAAAAEAEEAEEEEAE/</EEEEAEEEEAAEEEEEEEEEEE6EE<6EEEEEEEEAEEE///EAEEEE<AEEE#E +@NS500801:189:HWGFJBGX5:1:11101:24308:1119 1:N:0:ACAGTG +CACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGGCGGTTCACCCCTCCTTAGGCAACCNG ++ +AAAAAEAAEE/EAA/AE//EE6/EEAEEEEE<EE<EEEEEEEEE6<E/////E/E//E</A<EEEE6E6EEEEE#A +@NS500801:189:HWGFJBGX5:1:11101:3766:1118 2:N:0:ACAGTG +ACCACACCTTNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTGAAGTCATTTTTCCTTNNNNNNNNNNNNNNN ++ +/AAAAEEE6E#EE############################EEEEEEEEEEEEAEEEEEAE############### +@NS500801:189:HWGFJBGX5:1:11101:25700:1118 2:N:0:ACAGTG +GCCGCATCTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGGTGAAGGTCGGTGTGNNNNNNNNNNNNNNN ++ +AAAAAEEEE6#E/############################/EEA/EE6/EEEEE6E/AEE############### +@NS500801:189:HWGFJBGX5:1:11101:24308:1119 2:N:0:ACAGTG +GGAGGATCGCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATGCCGATCGGGTGTCCGCNNNNNNNNNNNNNNN ++ +A//AA/EEEE#EE###########################/E//AAEAEE//EEEE<EA/E###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_f.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:3766:1118 1:N:0:ACAGTG +ATCCCATACTGCTCAAAATAATCTCGTAGGTGATGTTCTTCAGTGTCTTCTTTAATACCACCAACAAAGATCTTNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE#E +@NS500801:189:HWGFJBGX5:1:11101:25700:1118 1:N:0:ACAGTG +GTGCCGTTGAATTTGCCGTGAGTGGAGTCATACTGGAACATGTAGACCATGTAGTTGAGGTCAATGAAGGGGTCNT ++ +AAAAAAAEAEEAEEEEAE/</EEEEAEEEEAAEEEEEEEEEEE6EE<6EEEEEEEEAEEE///EAEEEE<AEEE#E +@NS500801:189:HWGFJBGX5:1:11101:24308:1119 1:N:0:ACAGTG +CACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGGCGGTTCACCCCTCCTTAGGCAACCNG ++ +AAAAAEAAEE/EAA/AE//EE6/EEAEEEEE<EE<EEEEEEEEE6<E/////E/E//E</A<EEEE6E6EEEEE#A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_r.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:3766:1118 2:N:0:ACAGTG +ACCACACCTTNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTGAAGTCATTTTTCCTTNNNNNNNNNNNNNNN ++ +/AAAAEEE6E#EE############################EEEEEEEEEEEEAEEEEEAE############### +@NS500801:189:HWGFJBGX5:1:11101:25700:1118 2:N:0:ACAGTG +GCCGCATCTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGGTGAAGGTCGGTGTGNNNNNNNNNNNNNNN ++ +AAAAAEEEE6#E/############################/EEA/EE6/EEEEE6E/AEE############### +@NS500801:189:HWGFJBGX5:1:11101:24308:1119 2:N:0:ACAGTG +GGAGGATCGCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATGCCGATCGGGTGTCCGCNNNNNNNNNNNNNNN ++ +A//AA/EEEE#EE###########################/E//AAEAEE//EEEE<EA/E###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,24 @@ +@NS500801:189:HWGFJBGX5:1:11101:15584:1117 1:N:0:TGACCA +GTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEA#E +@NS500801:189:HWGFJBGX5:1:11101:26457:1117 1:N:0:TGACCA +CTTTTACAGTAACTCCGGGCATCGTGCGGCCTCCGCGCTGCCAGCCAGGGGAAAGGGAACGACGGGGTTTCCCGNG ++ +/AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEE6EEEEEEEEEEEEEEEEEEEAE#E +@NS500801:189:HWGFJBGX5:1:11101:25352:1117 1:N:0:TGACCA +GTCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCNG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEA#E +@NS500801:189:HWGFJBGX5:1:11101:15584:1117 2:N:0:TGACCA +GTAAGAACAANCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACTAACTAGAAAACTTCNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEE############### +@NS500801:189:HWGFJBGX5:1:11101:26457:1117 2:N:0:TGACCA +GCGAGACTCGNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCCTTTCCCCTGGCTGNNNNNNNNNNNNNNN ++ +AAAAAEEEEE##E############################EEEE/EEEEEEEEEEEEAAE############### +@NS500801:189:HWGFJBGX5:1:11101:25352:1117 2:N:0:TGACCA +GGGGGACCACNAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTCGGAAACGGAGCAGGTCNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEA###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_f.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:15584:1117 1:N:0:TGACCA +GTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEA#E +@NS500801:189:HWGFJBGX5:1:11101:26457:1117 1:N:0:TGACCA +CTTTTACAGTAACTCCGGGCATCGTGCGGCCTCCGCGCTGCCAGCCAGGGGAAAGGGAACGACGGGGTTTCCCGNG ++ +/AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEE6EEEEEEEEEEEEEEEEEEEAE#E +@NS500801:189:HWGFJBGX5:1:11101:25352:1117 1:N:0:TGACCA +GTCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCNG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEA#E
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_r.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:15584:1117 2:N:0:TGACCA +GTAAGAACAANCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACTAACTAGAAAACTTCNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEE############### +@NS500801:189:HWGFJBGX5:1:11101:26457:1117 2:N:0:TGACCA +GCGAGACTCGNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCCTTTCCCCTGGCTGNNNNNNNNNNNNNNN ++ +AAAAAEEEEE##E############################EEEE/EEEEEEEEEEEEAAE############### +@NS500801:189:HWGFJBGX5:1:11101:25352:1117 2:N:0:TGACCA +GGGGGACCACNAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTCGGAAACGGAGCAGGTCNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEA###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,24 @@ +@NS500801:189:HWGFJBGX5:1:11101:7257:1118 1:N:0:GATCAG +CCTAATAAAACTATAGAGCATTATCCCACCATGGTAGCAAATATGGCCCACAAAGGGATAAAAACTTCAATCACNC ++ +AA/AAAEE66EEEAEEEA/EEAEEE<EEEEEE/EEEAEEEEEEEEEEEEEEEEEE/<E/EAEEEAAEAEAEEEA#< +@NS500801:189:HWGFJBGX5:1:11101:6563:1118 1:N:0:GATCAG +CCAGCTTTTTCACACGAAGTTTGTGATTTCTGGCCTGGCGAAGAATGGTATTCCTGCGCATAGTCTTGGCGTAANG ++ +AAAAAEEEEEEAEE/EEEAEAEEEEEEEEEEEEE<EEEEEEEAEEEEAEEEEEEEE/EEEEEEEEEA/AEA/EE#A +@NS500801:189:HWGFJBGX5:1:11101:14965:1119 1:N:0:GATCAG +CGATCTTGAGCATTTTCCAGGCCAGTTTTAGGAGCAAAGCCATTTTCAACTAATGGAGGACCTAGGAGCTCTTTNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/E6#E +@NS500801:189:HWGFJBGX5:1:11101:7257:1118 2:N:0:GATCAG +ATAAAATGTANTANNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACCAGAATAACTGCATCNNNNNNNNNNNNNNN ++ +AAAAAE66AA#EE############################EEEEEE/<AE/EEE/AAEEE############### +@NS500801:189:HWGFJBGX5:1:11101:6563:1118 2:N:0:GATCAG +GAAGAAGAATNCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACCCTTACGCCAAGACTNNNNNNNNNNNNNNN ++ +AAAA/EE/EE#/A############################EEA/EEEEEEEE/EAE</EE############### +@NS500801:189:HWGFJBGX5:1:11101:14965:1119 2:N:0:GATCAG +GCCTTACTGGNATNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTGCTAAGAAATGTGTANNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE###########################EEEEEEEEEEEEEEEEEEEEE###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_f.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:7257:1118 1:N:0:GATCAG +CCTAATAAAACTATAGAGCATTATCCCACCATGGTAGCAAATATGGCCCACAAAGGGATAAAAACTTCAATCACNC ++ +AA/AAAEE66EEEAEEEA/EEAEEE<EEEEEE/EEEAEEEEEEEEEEEEEEEEEE/<E/EAEEEAAEAEAEEEA#< +@NS500801:189:HWGFJBGX5:1:11101:6563:1118 1:N:0:GATCAG +CCAGCTTTTTCACACGAAGTTTGTGATTTCTGGCCTGGCGAAGAATGGTATTCCTGCGCATAGTCTTGGCGTAANG ++ +AAAAAEEEEEEAEE/EEEAEAEEEEEEEEEEEEE<EEEEEEEAEEEEAEEEEEEEE/EEEEEEEEEA/AEA/EE#A +@NS500801:189:HWGFJBGX5:1:11101:14965:1119 1:N:0:GATCAG +CGATCTTGAGCATTTTCCAGGCCAGTTTTAGGAGCAAAGCCATTTTCAACTAATGGAGGACCTAGGAGCTCTTTNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/E6#E
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/4_r.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,12 @@ +@NS500801:189:HWGFJBGX5:1:11101:7257:1118 2:N:0:GATCAG +ATAAAATGTANTANNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACCAGAATAACTGCATCNNNNNNNNNNNNNNN ++ +AAAAAE66AA#EE############################EEEEEE/<AE/EEE/AAEEE############### +@NS500801:189:HWGFJBGX5:1:11101:6563:1118 2:N:0:GATCAG +GAAGAAGAATNCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACCCTTACGCCAAGACTNNNNNNNNNNNNNNN ++ +AAAA/EE/EE#/A############################EEA/EEEEEEEE/EAE</EE############### +@NS500801:189:HWGFJBGX5:1:11101:14965:1119 2:N:0:GATCAG +GCCTTACTGGNATNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTGCTAAGAAATGTGTANNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE###########################EEEEEEEEEEEEEEEEEEEEE###############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cat_wrapper_out1.bed Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,133 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + +chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cat_wrapper_out2.bed Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,135 @@ +# 1.bed +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +# 2.bed +chr1 147962192 147962580 NM_005997_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + +chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cat_wrapper_out3.bed Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,131 @@ +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chr1 147984545 147984630 BC007833_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 AJ011123_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 NM_002796_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 AY029205_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 AK057832_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 NM_000040_cds_1_0_chr11_116206509_f 0 + +chr11 116211733 116212337 BC005380_cds_0_0_chr11_116211734_r 0 - +chr11 130745911 130745993 AY358331_cds_0_0_chr11_130745912_f 0 + +chr12 38440094 38440321 NM_052885_cds_0_0_chr12_38440095_r 0 - +chr12 38905200 38905351 AY792511_cds_0_0_chr12_38905201_f 0 + +chr13 112381694 112381953 NM_207440_cds_1_0_chr13_112381695_f 0 + +chr13 29680676 29680875 NM_032116_cds_0_0_chr13_29680677_r 0 - +chr14 98521864 98521922 U88895_cds_0_0_chr14_98521865_f 0 + +chr14 98710240 98712285 NM_022898_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 BX537418_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 AK223365_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 NM_153700_cds_0_0_chr15_41679162_r 0 - +chr15 41773540 41773689 AK223365_cds_0_0_chr15_41773541_f 0 + +chr16 142908 143003 NM_005332_cds_0_0_chr16_142909_f 0 + +chr16 179197 179339 BC065198_cds_0_0_chr16_179198_r 0 - +chr16 244413 244681 AK057165_cds_2_0_chr16_244414_f 0 + +chr16 259268 259383 AB016929_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 NM_001792_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 NM_012397_cds_1_0_chr18_59406882_f 0 + +chr18 59455932 59456337 AB046400_cds_0_0_chr18_59455933_r 0 - +chr18 59528407 59528575 AY792326_cds_0_0_chr18_59528408_f 0 + +chr19 59068595 59069564 BC013995_cds_1_0_chr19_59068596_f 0 + +chr19 59236026 59236146 NM_198481_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 NM_004542_cds_0_0_chr19_59297999_f 0 + +chr19 59318205 59318718 AK128544_cds_3_0_chr19_59318206_r 0 - +chr2 118288583 118288668 NM_006773_cds_0_0_chr2_118288584_f 0 + +chr2 118390395 118390500 BC005078_cds_0_0_chr2_118390396_r 0 - +chr2 220108689 220109267 AY125465_cds_0_0_chr2_220108690_f 0 + +chr2 220229609 220230869 NM_024536_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 NM_181466_cds_0_0_chr20_33330414_r 0 - +chr20 33485370 33486123 BC085019_cds_1_0_chr20_33485371_f 0 + +chr20 33488491 33489122 NM_000557_cds_1_0_chr20_33488492_r 0 - +chr20 33513606 33513792 AF022655_cds_1_0_chr20_33513607_f 0 + +chr21 32687402 32687588 NM_032910_cds_0_0_chr21_32687403_f 0 + +chr21 32869641 32870022 NM_018277_cds_3_0_chr21_32869642_r 0 - +chr21 33321040 33322012 NM_005806_cds_1_0_chr21_33321041_f 0 + +chr21 33728358 33728724 AK129657_cds_0_0_chr21_33728359_r 0 - +chr22 30120223 30120265 NM_004147_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 BC032941_cds_0_0_chr22_30160420_r 0 - +chr22 30228824 30228916 NM_001007467_cds_1_0_chr22_30228825_f 0 + +chr22 30340151 30340376 CR456540_cds_0_0_chr22_30340152_r 0 - +chr5 131311206 131311254 AF099740_cds_11_0_chr5_131311207_r 0 - +chr5 131424298 131424460 NM_000588_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 BC035813_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 BC003096_cds_0_0_chr5_131621327_f 0 + +chr6 108299600 108299744 NM_007214_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 NM_003269_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 NM_003795_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 NM_145315_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 AF467257_cds_1_0_chr7_113660518_f 0 + +chr7 116512159 116512389 NM_003391_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 NM_000492_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 AF377960_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 NM_000127_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 BC051300_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 NM_014908_cds_0_0_chr9_128787520_r 0 - +chr9 128789552 128789584 NM_015354_cds_0_0_chr9_128789553_f 0 + +chr9 128850516 128850624 AB058751_cds_0_0_chr9_128850517_r 0 - +chrX 122745047 122745924 NM_001167_cds_1_0_chrX_122745048_f 0 + +chrX 152648964 152649196 NM_000425_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 AF101728_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 BC052303_cds_0_0_chrX_152694030_r 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/f.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,36 @@ +@NS500801:189:HWGFJBGX5:1:11101:3766:1118 1:N:0:ACAGTG +ATCCCATACTGCTCAAAATAATCTCGTAGGTGATGTTCTTCAGTGTCTTCTTTAATACCACCAACAAAGATCTTNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE#E +@NS500801:189:HWGFJBGX5:1:11101:25700:1118 1:N:0:ACAGTG +GTGCCGTTGAATTTGCCGTGAGTGGAGTCATACTGGAACATGTAGACCATGTAGTTGAGGTCAATGAAGGGGTCNT ++ +AAAAAAAEAEEAEEEEAE/</EEEEAEEEEAAEEEEEEEEEEE6EE<6EEEEEEEEAEEE///EAEEEE<AEEE#E +@NS500801:189:HWGFJBGX5:1:11101:24308:1119 1:N:0:ACAGTG +CACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGGCGGTTCACCCCTCCTTAGGCAACCNG ++ +AAAAAEAAEE/EAA/AE//EE6/EEAEEEEE<EE<EEEEEEEEE6<E/////E/E//E</A<EEEE6E6EEEEE#A +@NS500801:189:HWGFJBGX5:1:11101:15584:1117 1:N:0:TGACCA +GTTGATTCATAAAATTGTTTTTAGGTAGCTCGTTTGGTTTCGGGGTTTCTAGCTGTAATTCTTTTAGTTAGAAGNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEA#E +@NS500801:189:HWGFJBGX5:1:11101:26457:1117 1:N:0:TGACCA +CTTTTACAGTAACTCCGGGCATCGTGCGGCCTCCGCGCTGCCAGCCAGGGGAAAGGGAACGACGGGGTTTCCCGNG ++ +/AAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE/EEEEE6EEEEEEEEEEEEEEEEEEEAE#E +@NS500801:189:HWGFJBGX5:1:11101:25352:1117 1:N:0:TGACCA +GTCCAGGCTGGAGTGCAGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCNG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEA#E +@NS500801:189:HWGFJBGX5:1:11101:7257:1118 1:N:0:GATCAG +CCTAATAAAACTATAGAGCATTATCCCACCATGGTAGCAAATATGGCCCACAAAGGGATAAAAACTTCAATCACNC ++ +AA/AAAEE66EEEAEEEA/EEAEEE<EEEEEE/EEEAEEEEEEEEEEEEEEEEEE/<E/EAEEEAAEAEAEEEA#< +@NS500801:189:HWGFJBGX5:1:11101:6563:1118 1:N:0:GATCAG +CCAGCTTTTTCACACGAAGTTTGTGATTTCTGGCCTGGCGAAGAATGGTATTCCTGCGCATAGTCTTGGCGTAANG ++ +AAAAAEEEEEEAEE/EEEAEAEEEEEEEEEEEEE<EEEEEEEAEEEEAEEEEEEEE/EEEEEEEEEA/AEA/EE#A +@NS500801:189:HWGFJBGX5:1:11101:14965:1119 1:N:0:GATCAG +CGATCTTGAGCATTTTCCAGGCCAGTTTTAGGAGCAAAGCCATTTTCAACTAATGGAGGACCTAGGAGCTCTTTNT ++ +AAAAAEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA/E6#E
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/r.fastq Tue Jul 09 09:51:52 2019 -0400 @@ -0,0 +1,36 @@ +@NS500801:189:HWGFJBGX5:1:11101:3766:1118 2:N:0:ACAGTG +ACCACACCTTNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNAACTGAAGTCATTTTTCCTTNNNNNNNNNNNNNNN ++ +/AAAAEEE6E#EE############################EEEEEEEEEEEEAEEEEEAE############### +@NS500801:189:HWGFJBGX5:1:11101:25700:1118 2:N:0:ACAGTG +GCCGCATCTTNTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAATGGTGAAGGTCGGTGTGNNNNNNNNNNNNNNN ++ +AAAAAEEEE6#E/############################/EEA/EE6/EEEEE6E/AEE############### +@NS500801:189:HWGFJBGX5:1:11101:24308:1119 2:N:0:ACAGTG +GGAGGATCGCNTGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATGCCGATCGGGTGTCCGCNNNNNNNNNNNNNNN ++ +A//AA/EEEE#EE###########################/E//AAEAEE//EEEE<EA/E############### +@NS500801:189:HWGFJBGX5:1:11101:15584:1117 2:N:0:TGACCA +GTAAGAACAANCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACTAACTAGAAAACTTCNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEE############### +@NS500801:189:HWGFJBGX5:1:11101:26457:1117 2:N:0:TGACCA +GCGAGACTCGNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTTCCCTTTCCCCTGGCTGNNNNNNNNNNNNNNN ++ +AAAAAEEEEE##E############################EEEE/EEEEEEEEEEEEAAE############### +@NS500801:189:HWGFJBGX5:1:11101:25352:1117 2:N:0:TGACCA +GGGGGACCACNAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTCGGAAACGGAGCAGGTCNNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE############################EEEEEEEEEEAEEEEEEEEA############### +@NS500801:189:HWGFJBGX5:1:11101:7257:1118 2:N:0:GATCAG +ATAAAATGTANTANNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACCAGAATAACTGCATCNNNNNNNNNNNNNNN ++ +AAAAAE66AA#EE############################EEEEEE/<AE/EEE/AAEEE############### +@NS500801:189:HWGFJBGX5:1:11101:6563:1118 2:N:0:GATCAG +GAAGAAGAATNCANNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAACCCTTACGCCAAGACTNNNNNNNNNNNNNNN ++ +AAAA/EE/EE#/A############################EEA/EEEEEEEE/EAE</EE############### +@NS500801:189:HWGFJBGX5:1:11101:14965:1119 2:N:0:GATCAG +GCCTTACTGGNATNNNNNNNNNNNNNNNNNNNNNNNNNNNGCAACTGCTAAGAAATGTGTANNNNNNNNNNNNNNN ++ +AAAAAEEEEE#EE###########################EEEEEEEEEEEEEEEEEEEEE###############