Galaxy |

Changeset 0:f80c9e6700ba (2017-05-16)

Commit message:
planemo upload commit 91a780909d1eda07d17f6aebf7f08f0c024b6a25

added:
README.md
repository_dependencies.xml
test-data/chr4_part.500k_size.counts
test-data/chr4_part.ascii.counts
test-data/chr4_part.custom_unit.counts
test-data/chr4_part.fa
test-data/chr4_part.oascii.counts
test-data/contigs.advanced_wm.bed
test-data/contigs.fa
test-data/contigs.interval
test-data/contigs.nodust_wm.bed
test-data/contigs.seqid_wm.bed
test-data/contigs.wm.asn1
test-data/contigs.wm.asnb
test-data/contigs.wm.bed
test-data/contigs.wm.fa
test-data/contigs.wm.xml
tool_dependencies.xml
windowmasker_macros.xml
windowmasker_mkcounts.xml
windowmasker_to_bed.pl
windowmasker_ustat.xml

diff -r 000000000000 -r f80c9e6700ba README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Tue May 16 13:18:12 2017 -0400

[

@@ -0,0 +1,33 @@
+WindowMasker
+------------
+
+This is a Galaxy Wrapper for WindowMasker. WindowMasker is a program that can mask out highly repetitive and low complexity DNA sequences within a genome using the sequence of the genome itself.
+
+The WinMask module works in two stages. During Stage 1, unit counts are collected and stored in a separate file. During Stage 2 that file is used to mask the input sequences. Usually the unit counts file is created once per genome and then used multiple times for masking.
+
+WindowMasker_mkcounts
+======================
+Stage 1: Generate a counts file
+
+    $ windowmasker -mk_counts [-in input_file_name] [-out output_file_name] [-checkdup check_duplicates] [-t_low T_low] [-t_high T_high] [-fa_list input_is_a_list] [-mem available_memory] [-unit unit_length] [-genome_size genome_size] [-exclude_ids exclide_id_list] [-ids id_list] [-infmt input_format] [-sformat unit_counts_format] [-smem available_memory] [-use_ba use_bit_arrays]
+
+
+WindowMasker_ustat
+===================
+Stage 2: WindowMasker reads the data generated in Stage 1 and a set of input DNA sequences to output information about masked subintervals. If "-dust true" is specified, then the corresponding algorithm of the DUST module is applied to the input sequences in addition to window based masking. When DUST module is run, the results of the DUST and WinMask modules are merged together in the output. Specifically, a base is masked if it is masked by either DUST or by WinMask.
+
+    windowmasker -ustat unit_counts [-in input_file_name] [-out output_file_name] [-window window_size] [-t_thres T_threshold] [-t_extend T_extend] [-t_low T_low] [-t_high T_high] [-set_t_low score] [-set_t_high score] [-infmt input_format] [-outfmt output_format] [-dust use_dust] [-exclude_ids exclude_id_list] [-ids id_list] [-text_match text_match_ids] [-use_ba use_bit_arrays]
+
+Output formats:
+* Use the binary or text maskinfo ASN.1 output formats to generate the mask file for the NCBI BLAST+ makeblastdb tool
+* Use the BED output format to generate a list of masked regions
+
+Reference
+==========
+[NCBI C++ Toolkit Cross Reference -- WindowMasker](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/README)
+
+Citation
+=========
+
+[1] Morgulis A, Gertz EM, Schaffer AA, Agarwala R. WindowMasker:
+    Window based masker for sequence genomes. Submitted for publication.
\ No newline at end of file

diff -r 000000000000 -r f80c9e6700ba repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Tue May 16 13:18:12 2017 -0400

@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="Datatype definitions for NCBI BLAST">
+ <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>

diff -r 000000000000 -r f80c9e6700ba test-data/chr4_part.500k_size.counts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr4_part.500k_size.counts Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,133020 @@\n+##windowmasker-statistics-format-version:oascii 1.0.0\n+##windowmasker-statistics-algorithm-version:1.0.0\n+##parameters:unit=9 t_low=3 t_high=20\n+AAAA\n+9\n+1938 17 0 2\n+3\n+10\n+14\n+20\n+2\n+10\n+61\n+81\n+18\n+26\n+13\n+61\n+34\n+17\n+29\n+49\n+42\n+50\n+45\n+81\n+58\n+25\n+17\n+61\n+66\n+29\n+0\n+25\n+13\n+0\n+0\n+25\n+74\n+0\n+21\n+57\n+82\n+13\n+0\n+17\n+13\n+0\n+0\n+13\n+25\n+17\n+21\n+13\n+49\n+0\n+53\n+41\n+90\n+33\n+29\n+81\n+37\n+13\n+17\n+21\n+98\n+0\n+33\n+53\n+106\n+114\n+61\n+81\n+122\n+130\n+25\n+33\n+33\n+13\n+0\n+21\n+13\n+0\n+0\n+13\n+138\n+16777229\n+21\n+57\n+33\n+146\n+13\n+13\n+13\n+13\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+29\n+154\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+25\n+16777233\n+13\n+0\n+45\n+0\n+0\n+17\n+25\n+0\n+0\n+0\n+0\n+0\n+17\n+29\n+29\n+0\n+17\n+33\n+162\n+13\n+37\n+17\n+13\n+0\n+0\n+0\n+170\n+16777229\n+0\n+0\n+13\n+178\n+21\n+21\n+186\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+194\n+17\n+0\n+33\n+16777229\n+13\n+0\n+13\n+0\n+0\n+0\n+13\n+202\n+0\n+0\n+21\n+37\n+0\n+13\n+41\n+0\n+0\n+0\n+17\n+17\n+13\n+25\n+37\n+25\n+0\n+17\n+49\n+210\n+29\n+21\n+81\n+218\n+226\n+13\n+0\n+234\n+16777229\n+0\n+37\n+242\n+250\n+61\n+81\n+258\n+0\n+0\n+21\n+17\n+0\n+0\n+0\n+266\n+16777229\n+0\n+21\n+29\n+0\n+21\n+29\n+45\n+274\n+13\n+33\n+282\n+0\n+13\n+0\n+21\n+13\n+0\n+25\n+290\n+0\n+29\n+81\n+298\n+29\n+25\n+73\n+306\n+17\n+29\n+21\n+314\n+322\n+17\n+73\n+330\n+338\n+49\n+65\n+346\n+354\n+25\n+41\n+362\n+0\n+13\n+29\n+33\n+21\n+13\n+13\n+370\n+16777233\n+0\n+45\n+13\n+29\n+0\n+13\n+0\n+0\n+0\n+0\n+17\n+0\n+0\n+0\n+13\n+0\n+13\n+25\n+33\n+0\n+0\n+13\n+13\n+0\n+0\n+17\n+0\n+0\n+0\n+13\n+17\n+0\n+0\n+21\n+53\n+17\n+13\n+37\n+0\n+0\n+17\n+0\n+13\n+0\n+0\n+17\n+21\n+25\n+0\n+73\n+17\n+21\n+0\n+29\n+13\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+21\n+21\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+13\n+0\n+0\n+17\n+0\n+0\n+0\n+0\n+13\n+0\n+17\n+25\n+17\n+0\n+17\n+378\n+0\n+0\n+21\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+29\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+21\n+17\n+0\n+0\n+25\n+13\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+21\n+0\n+0\n+13\n+33\n+17\n+13\n+0\n+0\n+13\n+0\n+0\n+0\n+13\n+0\n+13\n+386\n+0\n+0\n+29\n+394\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+402\n+0\n+0\n+0\n+410\n+0\n+0\n+13\n+21\n+37\n+0\n+0\n+0\n+13\n+0\n+0\n+17\n+13\n+13\n+13\n+418\n+17\n+0\n+45\n+0\n+13\n+0\n+0\n+17\n+0\n+13\n+0\n+0\n+13\n+0\n+57\n+426\n+0\n+25\n+37\n+13\n+0\n+0\n+0\n+29\n+0\n+13\n+17\n+13\n+0\n+0\n+41\n+434\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+21\n+0\n+13\n+0\n+0\n+0\n+0\n+13\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+13\n+17\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+29\n+0\n+13\n+25\n+41\n+0\n+21\n+25\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+17\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+21\n+25\n+0\n+0\n+0\n+0\n+16777229\n+0\n+0\n+0\n+17\n+0\n+0\n+29\n+33\n+17\n+21\n+13\n+13\n+0\n+0\n+13\n+0\n+0\n+0\n+21\n+442\n+0\n+17\n+17\n+13\n+17\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+25\n+0\n+0\n+17\n+17\n+0\n+0\n+29\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+450\n+25\n+13\n+29\n+21\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+77\n+29\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+17\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+37\n+13\n+17\n+65\n+29\n+25\n+17\n+0\n+41\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+29\n+458\n+13\n+37\n+0\n+466\n+13\n+29\n+81\n+474\n+17\n+0\n+17\n+41\n+17\n+17\n+29\n+482\n+0\n+41\n+81\n+490\n+13\n+0\n+45\n+13\n+13\n+0\n+17\n+0\n+0\n+13\n+0\n+498\n+0\n+0\n+25\n+45\n+0\n+13\n+21\n+13\n+0\n+0\n+0\n+16777233\n+0\n+0\n+0\n+25\n+0\n+17\n+37\n+506\n+514\n+13\n+81\n+522\n+25\n+17\n+0\n+53\n+17\n+13\n+41\n+530\n+538\n+21\n+81\n+546\n+13\n+17\n+33\n+13\n+0\n+0\n+0\n+0\n+0\n+0\n+13\n+25\n+13\n+0\n+25\n+21\n+0\n+0\n+13\n+0\n+0\n+13\n+0\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+13\n+13\n+16777229\n+0\n+13\n+0\n+16777233\n+0\n+0\n+0\n+0\n+0\n+0\n+21\n+0\n+25\n+0\n+37\n+0\n+0\n+25\n+0\n+0\n+0\n+0\n+13\n+0\n+0\n+29\n+29\n+29\n+13\n+33\n+554\n+21\n+0\n+29\n+562\n+0\n+0\n+17\n+570\n+16777229\n+13\n+13\n+13\n+13\n+29\n+29\n+29\n+0\n+17\n+21\n+0\n+0\n+0\n+0\n+17\n+0\n+0\n+13\n+13\n+0\n+0\n+21\n+578\n+17\n+0\n+13\n+16777229\n+0\n+0\n+0\n+13\n+0\n+0\n+0\n+21\n+0\n+0\n+21\n+586\n+594\n+17\n+61\n+17\n+0\n+0\n+0\n+25\n+602\n+29\n+0\n+610\n+618\n+33\n+77\n+626\n+0\n+17\n+73\n+37\n+0\n+0\n+0\n+17\n+13\n+0\n+13\n+634\n+25\n+45\n+57\n+642\n+25\n+13\n+17\n+17\n+0\n+0\n+13\n+29\n+0\n+0\n+25\n+0\n+13\n+13\n+25\n+0\n+13\n+0\n+49\n+21\n+17\n+17\n+29\n+13\n+0\n+0\n+25\n+650\n+25\n+17\n+69\n+658\n+666\n+33\n+53\n+674\n+0\n+17\n+21\n+682\n+0\n+0\n+57\n+690\n+37\n+25\n+0\n+698\n+25\n+21\n+65\n+25\n+13\n+0\n+25\n+0\n+0\n+0\n+33\n+33\n+16777229\n+17\n+21\n'..b'8\n+13\n+515\n+4\n+516\n+3\n+515\n+9\n+520\n+7\n+524\n+20\n+515\n+3\n+520\n+18\n+517\n+20\n+516\n+9\n+516\n+20\n+517\n+6\n+515\n+3\n+515\n+5\n+519\n+15\n+516\n+20\n+515\n+7\n+515\n+5\n+515\n+5\n+516\n+3\n+520\n+18\n+516\n+11\n+518\n+20\n+515\n+7\n+515\n+4\n+515\n+4\n+520\n+7\n+515\n+3\n+515\n+3\n+515\n+3\n+516\n+3\n+515\n+4\n+515\n+7\n+516\n+4\n+517\n+3\n+515\n+12\n+515\n+3\n+515\n+5\n+516\n+3\n+515\n+3\n+516\n+5\n+517\n+4\n+515\n+3\n+515\n+3\n+516\n+5\n+516\n+4\n+516\n+9\n+515\n+6\n+515\n+3\n+515\n+5\n+516\n+14\n+515\n+6\n+516\n+20\n+515\n+6\n+515\n+7\n+516\n+10\n+515\n+5\n+516\n+8\n+521\n+20\n+516\n+9\n+517\n+16\n+515\n+4\n+515\n+3\n+516\n+12\n+516\n+5\n+515\n+15\n+515\n+14\n+516\n+5\n+516\n+11\n+517\n+12\n+515\n+5\n+515\n+3\n+515\n+7\n+515\n+3\n+516\n+5\n+516\n+6\n+516\n+3\n+517\n+15\n+517\n+9\n+515\n+4\n+522\n+9\n+516\n+20\n+515\n+5\n+516\n+7\n+516\n+19\n+516\n+20\n+516\n+6\n+515\n+3\n+515\n+3\n+516\n+7\n+516\n+3\n+515\n+3\n+516\n+9\n+516\n+5\n+516\n+8\n+515\n+6\n+515\n+5\n+515\n+5\n+516\n+5\n+515\n+6\n+515\n+8\n+516\n+7\n+515\n+3\n+515\n+5\n+520\n+4\n+516\n+5\n+516\n+3\n+515\n+5\n+520\n+20\n+516\n+11\n+519\n+11\n+515\n+9\n+519\n+14\n+515\n+6\n+516\n+10\n+516\n+16\n+516\n+8\n+515\n+3\n+518\n+14\n+516\n+12\n+520\n+10\n+518\n+7\n+516\n+3\n+515\n+4\n+515\n+6\n+518\n+8\n+515\n+4\n+515\n+5\n+516\n+10\n+516\n+8\n+516\n+10\n+515\n+5\n+518\n+6\n+527\n+20\n+518\n+5\n+519\n+20\n+515\n+16\n+516\n+3\n+516\n+19\n+516\n+5\n+522\n+20\n+515\n+14\n+522\n+7\n+515\n+3\n+515\n+3\n+517\n+4\n+515\n+3\n+517\n+4\n+516\n+10\n+517\n+3\n+515\n+7\n+517\n+6\n+521\n+3\n+519\n+20\n+517\n+10\n+516\n+20\n+517\n+13\n+515\n+4\n+515\n+6\n+520\n+20\n+517\n+5\n+519\n+20\n+532\n+20\n+521\n+9\n+520\n+5\n+532\n+9\n+524\n+4\n+519\n+4\n+517\n+6\n+519\n+3\n+532\n+15\n+518\n+4\n+521\n+4\n+524\n+5\n+520\n+9\n+519\n+3\n+518\n+3\n+518\n+3\n+520\n+4\n+519\n+3\n+516\n+5\n+520\n+4\n+532\n+10\n+520\n+3\n+528\n+5\n+516\n+5\n+517\n+4\n+516\n+4\n+522\n+6\n+531\n+6\n+516\n+3\n+515\n+4\n+529\n+11\n+522\n+5\n+517\n+5\n+516\n+4\n+518\n+4\n+516\n+7\n+515\n+4\n+518\n+3\n+521\n+3\n+523\n+4\n+515\n+3\n+516\n+3\n+516\n+3\n+532\n+11\n+516\n+3\n+530\n+12\n+515\n+3\n+527\n+11\n+515\n+3\n+524\n+14\n+519\n+5\n+516\n+3\n+516\n+4\n+519\n+7\n+527\n+5\n+527\n+4\n+516\n+6\n+520\n+7\n+525\n+8\n+523\n+6\n+517\n+3\n+520\n+10\n+517\n+4\n+515\n+4\n+522\n+4\n+516\n+5\n+518\n+3\n+515\n+3\n+515\n+3\n+515\n+3\n+516\n+3\n+519\n+5\n+516\n+3\n+516\n+3\n+516\n+5\n+517\n+3\n+515\n+3\n+519\n+3\n+532\n+16\n+525\n+10\n+523\n+5\n+520\n+4\n+530\n+4\n+523\n+6\n+519\n+5\n+515\n+3\n+516\n+3\n+526\n+5\n+518\n+3\n+528\n+5\n+515\n+4\n+517\n+7\n+518\n+3\n+529\n+4\n+515\n+3\n+519\n+3\n+515\n+5\n+517\n+4\n+519\n+6\n+517\n+3\n+515\n+3\n+515\n+3\n+528\n+4\n+522\n+3\n+521\n+6\n+519\n+3\n+516\n+4\n+515\n+3\n+532\n+9\n+517\n+4\n+522\n+4\n+515\n+6\n+523\n+13\n+517\n+6\n+515\n+8\n+518\n+5\n+521\n+3\n+526\n+3\n+515\n+3\n+522\n+3\n+518\n+4\n+518\n+6\n+523\n+5\n+516\n+4\n+515\n+3\n+515\n+5\n+518\n+5\n+518\n+8\n+518\n+5\n+515\n+6\n+517\n+3\n+516\n+6\n+516\n+5\n+515\n+3\n+516\n+3\n+516\n+3\n+516\n+3\n+515\n+3\n+515\n+3\n+517\n+4\n+516\n+4\n+516\n+3\n+517\n+3\n+516\n+4\n+517\n+3\n+532\n+10\n+518\n+5\n+532\n+5\n+519\n+5\n+519\n+3\n+522\n+6\n+520\n+4\n+515\n+3\n+520\n+7\n+516\n+3\n+515\n+4\n+520\n+3\n+524\n+4\n+515\n+3\n+526\n+8\n+520\n+3\n+527\n+4\n+519\n+4\n+528\n+4\n+518\n+3\n+517\n+6\n+525\n+6\n+523\n+5\n+517\n+4\n+515\n+3\n+517\n+7\n+515\n+3\n+516\n+3\n+529\n+11\n+525\n+6\n+529\n+5\n+516\n+3\n+520\n+5\n+523\n+6\n+524\n+3\n+522\n+4\n+517\n+4\n+521\n+3\n+515\n+3\n+518\n+3\n+515\n+4\n+522\n+6\n+519\n+5\n+515\n+4\n+532\n+8\n+516\n+4\n+517\n+4\n+515\n+3\n+515\n+3\n+520\n+3\n+532\n+16\n+518\n+8\n+524\n+6\n+515\n+4\n+516\n+6\n+516\n+4\n+531\n+18\n+519\n+3\n+523\n+12\n+522\n+12\n+518\n+4\n+515\n+6\n+515\n+5\n+517\n+6\n+516\n+3\n+515\n+3\n+515\n+4\n+515\n+4\n+522\n+4\n+515\n+6\n+515\n+3\n+516\n+4\n+519\n+14\n+515\n+3\n+515\n+3\n+516\n+3\n+518\n+4\n+515\n+3\n+515\n+12\n+517\n+3\n+522\n+4\n+515\n+7\n+517\n+4\n+515\n+4\n+516\n+3\n+519\n+7\n+516\n+3\n+515\n+5\n+516\n+3\n+516\n+6\n+516\n+4\n+524\n+4\n+516\n+4\n+523\n+5\n+517\n+4\n+516\n+3\n+517\n+4\n+516\n+4\n+516\n+3\n+517\n+3\n+516\n+3\n+517\n+3\n+520\n+5\n+516\n+5\n+521\n+4\n+519\n+6\n+515\n+3\n+517\n+4\n+515\n+4\n+520\n+4\n+515\n+6\n+520\n+5\n+516\n+4\n+518\n+4\n+525\n+3\n+516\n+3\n+519\n+8\n+520\n+3\n+517\n+3\n+515\n+4\n+526\n+10\n+517\n+3\n+518\n+3\n+532\n+11\n+532\n+5\n+516\n+4\n+516\n+3\n+527\n+4\n+519\n+4\n+516\n+4\n+529\n+4\n+518\n+6\n+516\n+3\n+517\n+3\n+532\n+13\n+516\n+3\n+523\n+5\n+522\n+6\n+515\n+6\n+519\n+3\n+516\n+6\n+518\n+4\n+515\n+5\n+531\n+4\n+515\n+3\n+524\n+3\n+516\n+3\n+515\n+5\n+519\n+6\n+518\n+3\n+516\n+3\n+532\n+3\n+515\n+3\n+531\n+5\n+518\n+5\n+518\n+5\n+518\n+3\n+518\n+3\n+518\n+4\n+515\n+3\n+515\n+3\n+524\n+3\n+517\n+5\n+518\n+3\n+520\n+3\n+518\n+3\n+516\n+3\n+515\n+4\n+523\n+3\n+515\n+3\n+522\n+4\n+532\n+10\n+518\n+3\n+532\n+5\n+518\n+3\n+532\n+6\n+519\n+4\n+522\n+3\n+523\n+4\n+517\n+3\n+522\n+3\n+529\n+4\n+532\n+12\n+524\n+5\n'

diff -r 000000000000 -r f80c9e6700ba test-data/chr4_part.ascii.counts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr4_part.ascii.counts Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,3304 @@\n+##windowmasker-statistics-format-version:ascii 1.0.0\n+##windowmasker-statistics-algorithm-version:1.0.0\n+##parameters:unit=8 t_low=8 t_high=52\n+8\n+0 52\n+1 39\n+2 30\n+3 52\n+4 39\n+5 17\n+6 11\n+7 30\n+8 25\n+a 18\n+b 37\n+c 52\n+d 21\n+e 32\n+f 52\n+10 37\n+11 17\n+13 31\n+14 17\n+15 10\n+17 13\n+18 8\n+1b 11\n+1c 18\n+1e 15\n+1f 21\n+20 31\n+22 8\n+23 17\n+24 10\n+28 17\n+29 8\n+2b 10\n+2c 24\n+2d 8\n+2e 22\n+2f 24\n+30 52\n+31 18\n+32 19\n+33 52\n+34 21\n+36 9\n+37 20\n+38 28\n+39 12\n+3a 15\n+3b 45\n+3c 52\n+3d 24\n+3e 35\n+3f 52\n+40 37\n+41 17\n+42 19\n+43 24\n+44 15\n+47 14\n+48 15\n+4b 11\n+4c 29\n+4d 9\n+4e 9\n+4f 31\n+50 16\n+51 8\n+53 12\n+5e 8\n+5f 15\n+60 16\n+64 10\n+6b 9\n+6c 11\n+6d 9\n+6f 9\n+70 16\n+72 8\n+73 17\n+74 9\n+78 9\n+79 16\n+7a 8\n+7b 13\n+7c 21\n+7e 10\n+7f 20\n+80 29\n+82 16\n+83 13\n+88 12\n+8c 8\n+8d 10\n+8e 8\n+8f 18\n+90 22\n+9c 16\n+9f 14\n+a0 20\n+a3 12\n+a4 10\n+ab 12\n+ac 13\n+af 8\n+b0 23\n+b1 10\n+b3 30\n+ba 13\n+bb 30\n+bc 21\n+be 13\n+bf 36\n+c0 52\n+c1 15\n+c2 25\n+c3 52\n+c4 23\n+c5 11\n+c7 12\n+c8 20\n+c9 8\n+cb 19\n+cc 52\n+cd 23\n+ce 30\n+cf 52\n+d0 29\n+d3 17\n+d4 11\n+d8 10\n+db 14\n+dc 18\n+de 14\n+df 25\n+e0 24\n+e1 13\n+e2 10\n+e3 20\n+e4 18\n+e6 8\n+e7 9\n+e8 15\n+eb 14\n+ec 35\n+ed 8\n+ee 18\n+ef 48\n+f0 52\n+f1 12\n+f2 11\n+f3 43\n+f4 18\n+f5 8\n+f6 15\n+f7 12\n+f8 18\n+f9 20\n+fa 12\n+fb 33\n+fc 52\n+fd 16\n+fe 25\n+ff 52\n+100 35\n+101 17\n+102 11\n+103 18\n+104 15\n+107 15\n+108 20\n+10b 9\n+10c 21\n+10d 9\n+10f 28\n+111 12\n+11f 9\n+120 14\n+124 10\n+127 8\n+12f 11\n+130 24\n+132 8\n+133 17\n+134 8\n+137 9\n+13c 12\n+13d 9\n+13f 37\n+140 17\n+141 9\n+143 10\n+14f 9\n+164 9\n+170 11\n+17b 8\n+17c 10\n+180 22\n+183 11\n+193 12\n+19f 13\n+1af 8\n+1b3 12\n+1c0 18\n+1c8 8\n+1cc 15\n+1cf 13\n+1d0 9\n+1dc 9\n+1e0 14\n+1e4 10\n+1e5 13\n+1e9 8\n+1ec 8\n+1ee 10\n+1ef 9\n+1f0 13\n+1f1 12\n+1f3 20\n+1f5 8\n+1f8 9\n+1fa 10\n+1fd 10\n+200 31\n+202 11\n+203 17\n+204 8\n+207 8\n+208 13\n+20b 9\n+20c 19\n+20f 15\n+210 11\n+213 11\n+223 8\n+230 9\n+233 12\n+234 8\n+23c 10\n+23f 14\n+240 18\n+241 8\n+242 9\n+243 11\n+248 9\n+24f 12\n+253 10\n+260 8\n+270 9\n+273 15\n+27c 9\n+27f 20\n+280 15\n+282 10\n+283 9\n+28b 8\n+28c 11\n+2ac 10\n+2af 9\n+2b0 8\n+2b3 11\n+2c0 22\n+2c1 8\n+2c2 12\n+2c3 14\n+2c4 10\n+2c7 10\n+2cc 9\n+2ce 23\n+2cf 16\n+2dc 8\n+2de 9\n+2e4 9\n+2eb 15\n+2ec 8\n+2ee 20\n+2ef 16\n+2f0 17\n+2f1 11\n+2f3 21\n+2f4 8\n+2f5 8\n+2f7 8\n+2fb 11\n+2fc 17\n+2fe 13\n+300 52\n+301 9\n+302 12\n+303 52\n+304 15\n+306 8\n+307 11\n+308 17\n+30b 15\n+30c 52\n+30d 9\n+30e 25\n+30f 50\n+310 17\n+311 8\n+313 27\n+314 9\n+317 8\n+31c 16\n+31f 17\n+320 18\n+323 11\n+328 9\n+32b 9\n+32c 11\n+32f 17\n+330 52\n+331 15\n+332 12\n+333 52\n+334 18\n+335 11\n+336 11\n+338 21\n+339 12\n+33b 27\n+33c 52\n+33d 18\n+33e 16\n+33f 52\n+340 29\n+341 8\n+342 8\n+343 25\n+34c 12\n+34d 10\n+34f 11\n+350 11\n+353 8\n+360 10\n+361 9\n+362 9\n+363 16\n+36d 8\n+36e 9\n+370 18\n+372 8\n+373 16\n+378 9\n+37b 14\n+37c 9\n+37d 9\n+37e 8\n+380 18\n+381 9\n+383 13\n+384 10\n+387 9\n+388 11\n+38e 9\n+38f 16\n+390 12\n+392 10\n+393 12\n+39f 13\n+3a0 19\n+3a3 8\n+3ac 9\n+3af 10\n+3b0 27\n+3b1 14\n+3b2 8\n+3b3 33\n+3b8 9\n+3b9 8\n+3ba 9\n+3bc 28\n+3bd 14\n+3be 20\n+3c0 52\n+3c2 12\n+3c3 38\n+3c4 13\n+3cc 35\n+3cd 10\n+3ce 21\n+3cf 46\n+3d0 19\n+3d1 9\n+3d3 11\n+3d7 9\n+3d8 13\n+3db 13\n+3dc 10\n+3dd 9\n+3de 11\n+3df 17\n+3e0 8\n+3e3 26\n+3e4 10\n+3e7 14\n+3e8 8\n+3eb 8\n+3ec 24\n+3ed 11\n+3ee 12\n+3ef 27\n+3f0 52\n+3f1 29\n+3f2 14\n+3f3 49\n+3f4 27\n+3f6 12\n+3f7 27\n+3f8 20\n+3fa 11\n+3fb 26\n+3fc 52\n+3fd 23\n+3fe 24\n+400 34\n+401 17\n+402 10\n+403 27\n+404 10\n+407 14\n+40b 15\n+40c 19\n+40d 12\n+40e 10\n+40f 13\n+410 15\n+412 12\n+413 9\n+41f 12\n+420 13\n+422 11\n+423 13\n+430 32\n+431 8\n+433 13\n+43c 14\n+43d 11\n+440 9\n+444 11\n+47c 9\n+480 9\n+483 15\n+490 12\n+493 8\n+4b0 11\n+4c0 13\n+4c1 12\n+4c2 8\n+4c3 13\n+4cc 9\n+4cf 17\n+4df 9\n+4f0 18\n+4f3 10\n+4f7 9\n+4fc 25\n+4fd 16\n+4fe 10\n+500 16\n+503 11\n+504 8\n+50c 13\n+50f 8\n+51f 10\n+5c0 14\n+5f0 13\n+600 13\n+601 8\n+603 15\n+607 10\n+60d 9\n+60f 8\n+64c 8\n+67d 8\n+6ac 16\n+6c0 8\n+6c3 9\n+6d8 12\n+700 15\n+703 14\n+70c 10\n+710 8\n+727 9\n+730 17\n+733 12\n+73b 8\n+73c 10\n+740 10\n+770 10\n+780 11\n+782 9\n+783 8\n+794 9\n+7b3 12\n+7c0 14\n+7c3 9\n+7c7 10\n+7cc 14\n+7cd 9\n+7ce 8\n+7cf 24\n+7d3 12\n+7e3 9\n+7ec 8\n+7f0 16\n+7f3 13\n+7f4 10\n+7f7 8\n+7fb 12\n+7fc 30\n+7fd 15\n+7fe 8\n+800 22\n+801 13\n+802 13\n+803 28\n+804 11\n+808 12\n+80'..b' 275\t51574\t100\n+# 276\t51574\t100\n+# 277\t51574\t100\n+# 278\t51574\t100\n+# 279\t51574\t100\n+# 280\t51574\t100\n+# 281\t51574\t100\n+# 282\t51574\t100\n+# 283\t51574\t100\n+# 284\t51574\t100\n+# 285\t51574\t100\n+# 286\t51574\t100\n+# 287\t51574\t100\n+# 288\t51574\t100\n+# 289\t51574\t100\n+# 290\t51574\t100\n+# 291\t51574\t100\n+# 292\t51574\t100\n+# 293\t51574\t100\n+# 294\t51574\t100\n+# 295\t51574\t100\n+# 296\t51574\t100\n+# 297\t51574\t100\n+# 298\t51574\t100\n+# 299\t51574\t100\n+# 300\t51574\t100\n+# 301\t51574\t100\n+# 302\t51574\t100\n+# 303\t51574\t100\n+# 304\t51574\t100\n+# 305\t51574\t100\n+# 306\t51574\t100\n+# 307\t51574\t100\n+# 308\t51574\t100\n+# 309\t51574\t100\n+# 310\t51574\t100\n+# 311\t51574\t100\n+# 312\t51574\t100\n+# 313\t51574\t100\n+# 314\t51574\t100\n+# 315\t51574\t100\n+# 316\t51574\t100\n+# 317\t51574\t100\n+# 318\t51574\t100\n+# 319\t51574\t100\n+# 320\t51574\t100\n+# 321\t51574\t100\n+# 322\t51574\t100\n+# 323\t51574\t100\n+# 324\t51574\t100\n+# 325\t51574\t100\n+# 326\t51574\t100\n+# 327\t51574\t100\n+# 328\t51574\t100\n+# 329\t51574\t100\n+# 330\t51574\t100\n+# 331\t51574\t100\n+# 332\t51574\t100\n+# 333\t51574\t100\n+# 334\t51574\t100\n+# 335\t51574\t100\n+# 336\t51574\t100\n+# 337\t51574\t100\n+# 338\t51574\t100\n+# 339\t51574\t100\n+# 340\t51574\t100\n+# 341\t51574\t100\n+# 342\t51574\t100\n+# 343\t51574\t100\n+# 344\t51574\t100\n+# 345\t51574\t100\n+# 346\t51574\t100\n+# 347\t51574\t100\n+# 348\t51574\t100\n+# 349\t51574\t100\n+# 350\t51574\t100\n+# 351\t51574\t100\n+# 352\t51574\t100\n+# 353\t51574\t100\n+# 354\t51574\t100\n+# 355\t51574\t100\n+# 356\t51574\t100\n+# 357\t51574\t100\n+# 358\t51574\t100\n+# 359\t51574\t100\n+# 360\t51574\t100\n+# 361\t51574\t100\n+# 362\t51574\t100\n+# 363\t51574\t100\n+# 364\t51574\t100\n+# 365\t51574\t100\n+# 366\t51574\t100\n+# 367\t51574\t100\n+# 368\t51574\t100\n+# 369\t51574\t100\n+# 370\t51574\t100\n+# 371\t51574\t100\n+# 372\t51574\t100\n+# 373\t51574\t100\n+# 374\t51574\t100\n+# 375\t51574\t100\n+# 376\t51574\t100\n+# 377\t51574\t100\n+# 378\t51574\t100\n+# 379\t51574\t100\n+# 380\t51574\t100\n+# 381\t51574\t100\n+# 382\t51574\t100\n+# 383\t51574\t100\n+# 384\t51574\t100\n+# 385\t51574\t100\n+# 386\t51574\t100\n+# 387\t51574\t100\n+# 388\t51574\t100\n+# 389\t51574\t100\n+# 390\t51574\t100\n+# 391\t51574\t100\n+# 392\t51574\t100\n+# 393\t51574\t100\n+# 394\t51574\t100\n+# 395\t51574\t100\n+# 396\t51574\t100\n+# 397\t51574\t100\n+# 398\t51574\t100\n+# 399\t51574\t100\n+# 400\t51574\t100\n+# 401\t51574\t100\n+# 402\t51574\t100\n+# 403\t51574\t100\n+# 404\t51574\t100\n+# 405\t51574\t100\n+# 406\t51574\t100\n+# 407\t51574\t100\n+# 408\t51574\t100\n+# 409\t51574\t100\n+# 410\t51574\t100\n+# 411\t51574\t100\n+# 412\t51574\t100\n+# 413\t51574\t100\n+# 414\t51574\t100\n+# 415\t51574\t100\n+# 416\t51574\t100\n+# 417\t51574\t100\n+# 418\t51574\t100\n+# 419\t51574\t100\n+# 420\t51574\t100\n+# 421\t51574\t100\n+# 422\t51574\t100\n+# 423\t51574\t100\n+# 424\t51574\t100\n+# 425\t51574\t100\n+# 426\t51574\t100\n+# 427\t51574\t100\n+# 428\t51574\t100\n+# 429\t51574\t100\n+# 430\t51574\t100\n+# 431\t51574\t100\n+# 432\t51574\t100\n+# 433\t51574\t100\n+# 434\t51574\t100\n+# 435\t51574\t100\n+# 436\t51574\t100\n+# 437\t51574\t100\n+# 438\t51574\t100\n+# 439\t51574\t100\n+# 440\t51574\t100\n+# 441\t51574\t100\n+# 442\t51574\t100\n+# 443\t51574\t100\n+# 444\t51574\t100\n+# 445\t51574\t100\n+# 446\t51574\t100\n+# 447\t51574\t100\n+# 448\t51574\t100\n+# 449\t51574\t100\n+# 450\t51574\t100\n+# 451\t51574\t100\n+# 452\t51574\t100\n+# 453\t51574\t100\n+# 454\t51574\t100\n+# 455\t51574\t100\n+# 456\t51574\t100\n+# 457\t51574\t100\n+# 458\t51574\t100\n+# 459\t51574\t100\n+# 460\t51574\t100\n+# 461\t51574\t100\n+# 462\t51574\t100\n+# 463\t51574\t100\n+# 464\t51574\t100\n+# 465\t51574\t100\n+# 466\t51574\t100\n+# 467\t51574\t100\n+# 468\t51574\t100\n+# 469\t51574\t100\n+# 470\t51574\t100\n+# 471\t51574\t100\n+# 472\t51574\t100\n+# 473\t51574\t100\n+# 474\t51574\t100\n+# 475\t51574\t100\n+# 476\t51574\t100\n+# 477\t51574\t100\n+# 478\t51574\t100\n+# 479\t51574\t100\n+# 480\t51574\t100\n+# 481\t51574\t100\n+# 482\t51574\t100\n+# 483\t51574\t100\n+# 484\t51574\t100\n+# 485\t51574\t100\n+# 486\t51574\t100\n+# 487\t51574\t100\n+# 488\t51574\t100\n+# 489\t51574\t100\n+# 490\t51574\t100\n+# 491\t51574\t100\n+# 492\t51574\t100\n+# 493\t51574\t100\n+# 494\t51574\t100\n+# 495\t51574\t100\n+# 496\t51574\t100\n+# 497\t51574\t100\n+# 498\t51574\t100\n+# 499\t51574\t100\n+# 500\t51574\t100\n+#\n+# 90%% threshold at 8\n+# 99%% threshold at 24\n+# 99.5%% threshold at 34\n+# 99.8%% threshold at 52\n+\n+>t_low 8\n+>t_extend 24\n+>t_threshold 34\n+>t_high 52\n+\n'

diff -r 000000000000 -r f80c9e6700ba test-data/chr4_part.custom_unit.counts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr4_part.custom_unit.counts Tue May 16 13:18:12 2017 -0400

diff -r 000000000000 -r f80c9e6700ba test-data/chr4_part.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr4_part.fa Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,2001 @@\n+>chr4:100000-200000\n+TAAATTTTATATGGTCGCAAAGGTTTTCTTTATTACGTTGCAGACTTCAG\n+AAAAAAGTCAATATATAGTCAAAAATGGTATTAAAATGTTTAAGATGCAA\n+TGCAATAAGAGTTTAGCAAGAGAGAATGCTATAGTCAATTTTCCCGTTAC\n+TCAGTAAAATTGAGAGAGTGGAATTGCACAATTTTTCTGGGATATCAATA\n+GATATTGGTCAATAAAATAAAAAAAAAAATTGTTTAAAAGTGTGGGAGTG\n+GTGGGGCGTGACCAAAGCGTTTTCGGCAAATCGAGACAAGCCTAATAAAA\n+ATATGAAAAAATAACAAATTCAATTCAATCATTTTCAAACGGTTTGTGGG\n+CGAAAGTGTTTTGACACATTTTGACACACCAATTCGAACGCCCAAAACTG\n+CCACGCCCAGACTTTTAAAAAATGTATTAATATTTTTTCACATTTTATTA\n+GATTTGTAAATTGCCACGTTTGTAAAGATTTGTAAAAATTAGGCTGCGCT\n+AACTCTAAACGGCCATTTTTTCTCATTTCATTCCTAACATCTATCGATAT\n+CCCAGAAAAAATATGAAATTTCGCGTTCGCATTCACACTAGCTGAGTAAC\n+GGGTATCTGATAGTCGGGGAACTAGACTATAGCATTCTGTCTTGTTTTAT\n+TTATTTTATAAATAATAACTTTAAAGAATGTGTGCTTGTATTATTTTAAA\n+ATGTATTTTCTTTTTTTCAATTTATGTTTTAAATTACAAAAGTAACAACA\n+ATTCCAAGTCGCAGCTCTATTTTATTTATAAGTTAATATATTTATGAACT\n+TAATATTAATATTAAAATTGATTTCTTCCCGAAAATCGTGTTTTAGTACA\n+AGCACGCACTCATAGACACCAGATATATGCATTAGTACACCGAAACTACA\n+AGTACACCGCATACACACACAGTATTTTTTGACTTTATACTTTATATGAT\n+CGAATACGCTTCCTTCTGCCTGTGACATACTTTTCAACAAATCTAGTATA\n+CCCTTTTACTCTACGAGTAACGGGTATAAAAATGCGACCTGTTTAATGCA\n+AAATGGCTAAATCAATTTCTTGAAGCACGACGTGCGGACAGAAACCCCCA\n+AGAAAAGATATCTACTCTTACTTTTCACACGTGGCAAGCTAAATACTCTA\n+TTGACAATTATTCTACTAAAAGGTCATTTTTGAAATTTATTTATGTGATA\n+GTATTGTACATAGCGTTAAGGCAATGCAAAGCAAGAATTTTTACATGGTG\n+CCAATTGATCAACAATAATATTGATTTAAAGTTTAAGTGAAATTTACAAT\n+GCATGAGCATACGTGTGCACACATACAGTTGTCGGCTGTCACTGCTGGCT\n+GTAGAGCTCTCCGCTTTCTGGCACTTGAATAAAAGTTCGAGAGAGCTGGA\n+TCCAGTTCTTAACCCAGTCAAAAAAAAAAAAATAAATAAATATCACGTTA\n+GAGAGCCAGCAGTGCTGTAGCTTGTATTATGAACCTTAAACGGCTAAGGA\n+TACCTGTATCGTCGGCAAATGTGGATGTGGATACTCTTAGGCAACTATTA\n+GGCGACGTTGCTGTATAGATGAGGTAAGAACTCTGCCTTGGGGGTGTTGC\n+ATCGCACTGCAAACTTTCTGGACGACTTAAGAATGTTCTGAGTTTTTACT\n+TTAAACATTAGGTCGTCGAGTCAGACTCTGTCGAATGCTTGGGATACGTC\n+TAAAAATACGGCTGTGTAGTACTCACGATTTTCGTATGCAGATCTTAGTT\n+TAGATTGTCGGGTTAGCAGGCATTTTTGAATACCTAACCAGACTTTGGAA\n+TCATTATGAAGATCGATCTTTTCCATCCTTCTGGGCAGAAACCAAGTTTG\n+GTGATGGTATTCAAGAGCTGAGTTATGTAGTGAACTGTAGAATGTGGGGC\n+AGCTCGATGATCATTTTTGGATCACATCTCAGCACATTTTTACGGGCTGA\n+GATTGTCTTTAACTAGACAGTTATTCCAATATAAAAATTTAGATTAGTAT\n+TACTAGAGACAATGCATTTATGTACATACACATATGTCCATAATTATTTG\n+CACGGTCGCAAGCCTCCCACTATTTTTTATTTTATTTATGTTAGGCATCT\n+ATGTATTTTAATTTTCTTTTGCAATCCCAATATCTAAGTAACTACCGAAA\n+CTATTGACGAAGTCGACTAAAACGGTGGAAAGACAATATTAAGTAACATA\n+AGTTTATTTGGGTATGTCCATATTGTGGCTTTGCCCACAGTCCGTAATAA\n+GTTTTAAATTTTGTAATAAATTTTTTTAGATAAAAATATATGTGCTCTCT\n+TCAGTTCAGTCAGAGGTTTCCAACGCAGTGAGAGGCATTTGTGACCATAT\n+GATGTATGTATTTTTAAGCAGTATGAACAAATCGATATATCCGTGACTTT\n+CTGGCCGTCCGTCTGTTTCTACTCATGATTTCATCATTATCGAACGACTA\n+TATAAAGTTAAAAGCTGTCATATGAACAATGTGAAAATTACTATCTAGTT\n+AGTTATTAAATAATGAATTGCTTTTTTTAATAAAACTACCTTTTTTATAG\n+CAATTAAATTGACACTTTCAAATAATACTGAAAAAAAATAATTAGTAAAA\n+AATTATCAGTATTAGGCATTTCACGTATATTAATTTTAAAGAGACAAATC\n+ATTCAATATTAAACTTTCATATTACATTACATACAATTTAAACATAGAAT\n+TACAATGCCTTCTAAAAATGTGCCGAACCAAATTATTATATAAAAGGATA\n+TCCCGTCACTTTTGAAACAACATTTACCGTAATACTGCAATTTTTACATC\n+TTGCGTGAATTTTGTTGATATAAACTGATAGATACTCTAATTAAAAAATG\n+ATTTTGCACCTGTTAGACCTATTATGAAATCGTCCACATTAAAAGACACT\n+GACCAAAAATCTCAGAACCACCCCCTTACATTTATCATACAATGATTAAG\n+TCCAAAAAAAGGACTACTATTATTAACTGCACGATATGCAACCCTATTTA\n+TCAATTTATAAGACCGAAAAACTCAAACTTTACTTATTATTTAGTTTTTA\n+TGTTTTTTAAATATTATTTATGCGTTTTAAATTTGTGGGAGGCACATTAA\n+ATCTAGTTGAAAATAAAATTATTATTTTCGTGGCACTAAAAATATTATTA\n+CAATGGCATGTAAAAACAAGAAAAAAGGCTCTATATATATATGGTATATC\n+CCTGAATATCAGATACCCGTTAATCACCTAGTGCAAACGCGAACGCGAAA\n+TTTCATCAGTTTTCGGGGATACCGATGGATATTGGGGAATAAATGAGAAA\n+AAAAATTAAAACTGTTCAAAAGTGTGGGCGTGACCTGTCGGTGGCACAAA\n+GTTTTTTGGTAAATCGATAGAAAATTTACAAGGTTAGAAAATTTTTTTAA\n+AAATATTAAAACGTTTTGCAAAAAAGGGCGTGGCAGTGATGGGCTGTATT\n+GGGGTTTTTTACAAATCGATAGAAATTTACAAGACTTCTTCTAGGTTTAA\n+TAGTTCCTGAGATCTCAGATCGACACGACTATTGATCCTGATCAAGAGTA\n+TATATACTTTATATGGTCGGAAACGCTTCCTTCTGCTTCAGTTACATACT\n+TTTCAACGAAACAAGTATACTCTTTTACTATACGAGTAACGGGTATAATT\n+ACAGTTCCTATTAATCAAGCCAAAATGTAGGCGCATGAACGTTTTATTTT\n+ATCTGGTGTTATTTGGTGTCCATGACCCTAAAAACAACACACTTCAAAAA\n+ACAAGCAGCAGTTTCGTTTTGTACTTTTCTAATTGGCAAGCAGATAAAAA\n+TATTAT'..b'AATGTTTAGATTTTTCTTATTTTTATTGTTTGTCTTGCTAATTTTT\n+ATCTATATACCACTGTGGCCATGGTTATCCTTTCACCAATAAAACGCCCT\n+AAAGGGTCACGGACGCACTTTTAAAAAATTGATTAAAATTTTGTCTCATA\n+TTATTCTCTAATATCTATAGAAACACCAGAAAATTATTAAATTTCACGTT\n+CGCATTGCCACTAGCTGAGTAAGCTGGGTATCTGATAGTCGCGGAACTCG\n+ACTATAGCATTATCTCTTGTTATATATGTATGTATGTTATAATTGTGTGA\n+TTTGTATAATTATTTATTCGTAGCCATGAATAATAAAGAAAAATGACATG\n+ATTGTCCGACCAGGTTCAATCCAACATACACAATAACCGCAATATATAAA\n+ATCCGTCAAAATATCCAATATAAGTTACGGTAAGATACTTATATTCCAAT\n+CCTTTTTACTAAATAATAAGTAAAGATATGTAAATGCTGTATTTAATATT\n+TATTTTTGCTTGGCTAGCTTATTTAAGGTAATTACATTCAAGAACATGCA\n+TACATGTTGCTTCTTTTTCAATGTGTACAAAGTTTATGAATAATTGTAAT\n+TCAGAAATATTCTTTGTAAATACTTATCATTATTATTCAGAGATATTAAT\n+ATTCCATATTAAAATTAAAATATGTACAGTGTATCTTTAATATTAATAAT\n+TTATGTATGGCTTCCTAATACGACAGTAAAATAATATTCTTACAATTGAA\n+CACCTAAATATAATTATTAATAAGGATCCGTATATTTTGGAAGATTTAAC\n+AATAGAAAATGCAATACCCTTAACTAATCAGTACTATGTAATTAACGTTT\n+AATTGTAACAGGCTTTTAACTTATATTAAACGAATTTAGGTTGTTGTAGT\n+CTTAAGAATTTTTTTATTTTTATAAGCCGATAAATATAAGAGTTGTACGA\n+CTCTAAAACTTATTTTGCAATATTATGTTATACGGCCTTTTTAAAATACT\n+TATCTTACATGAAAACCAATATTTCTTTTATGAACTTTAAACTGGCAAAA\n+TTATATTTTTTATATTTTTGTTCCATACATATGAGAACAAAATCAATTAT\n+TTTCATTTTACAAACTGCAAAAATTCAACTGAAATGATAATACAAAATAT\n+TTTTAAATCATAATCTAAAAATATCATGTTATATATTTAATTTTTCAAGT\n+TCGTATCCTGCATTAATCGGACCGCATACTTTTTTATAATAAATTTAATC\n+AGTATGTTACATTATTAATATGTTTTCGTGTAGAAATTCTGTGATCTTTT\n+TATTGAGTATATTATTATATACATATTTACTAGGTAAATAATTAATGGCT\n+GGAGACGTAATATACAGTTGCGAATGCTTGTTTTAATTTTGTTTTATGAA\n+ATGGATTTAGAACAAAATACATCTATGCAACGCGAAAATCAAATATAGAG\n+TTTCGTATTAAAACGTTTCTAAAATGATATTTTAAATAAATATATATTTT\n+TTAGAGTAGGCATTAGATAATTATATATCGAATGATAGGTTATAATTTTG\n+CTTTTCGCTAGTTTTGTTATATATTTATATATCACAAGTTTGAAGATAGT\n+TGAAAACGTCTATTTTACTACTTATTGACATAAAAGGACAATCAAAACCG\n+CGCTTGATTGATAGTGAGTTATAAAACAAGATAGTTATCGTTATGACATG\n+CAAAGCTATGAGTCGGAATTAAAAATCTTAGCAATCGATGCCATTTACCG\n+TCGCACTGCAACTTTTAAGACGAAGGGATAAAACTGCAGTCCTTTCGGAA\n+TCTACATTACTTCCGTTTTGAACACAATTTGGATCGTCTATGGACCGAAA\n+TCGTAGAAAGCCTTGGTCTGCTACAAGCATACTATCAGAAGCACTGGATG\n+TTGTGCATGAATTTGAAGATGCAGACGCCACTGAAGCTGATGAAGTCGTG\n+CATAACTCCGACCTATGCTTTCCATTATTTGGCATATGTAATTGTGCGCG\n+ATAATTGGAATTTTTAGTTGCCGCTGACCCGGCAAGTGATGGTGTTTTTG\n+TGTTCATAGATATAGAATTTGGTGCCGTATCTTCAACAGGAATGACAAAA\n+CCATGATCGTTATTTATCAAGTTTGTACACTCTACATTATTTCCCGATAT\n+AGTGTCATCTTCTTCATCTTCTTCATCCTCGGAATTGTGACCATAAGGTA\n+ACTGTTGTAGATGGTTCTCCCTTATGGGCATACTTTTAAACAGTTCAGTT\n+TCACTCTCCAATGACCTTAAGTTCGAATTACGTCCACTTGCTCTCTGGTA\n+ATACTGTGGTCTATCTTTATCTGGTATTCCTAACGTCTGCGATCCATTGG\n+CGACTATTCGTTGAGTTTCAGCAGAAGCAATTGGTGACTCAAGGGTTCGA\n+CCTAAAGCACCAGCCTTGGCTATACTGCTTATAGTACCACTTTTGCAAAC\n+GCCGTTGAAATATCCGCGTTCAAATGAATTAAAACTTCCAAATCGCCCAC\n+CACCTCCCAAATTTGATGAAGAGCACGAATTAGCTGAATTCGAACTGCGG\n+CGCTCATGAGTCTTGCTTTCAAAGACATGCCGATCAAGTGCACCGTTAAA\n+CTTTTTTTTGCGCCCATTTGTTATTTTTTGTCGGTCTTGAATACACTCAC\n+TGTTTGACTGAACATTGTGAACTGATTTTTCCTTAAACACCGGTCGCTCA\n+AAGATGTTAAATTCATATCTCTTGTTTTCCTGCTCTAGTGGTTCAGAATA\n+ACAATTGTTTTGCAACAATTCTACTTGCTGCTGCAAAGCCCCAGAATTTG\n+AGTTAAAAGAAACTTCATTTTGATCGTAATCCCTTCGCTTTTGTTCAGTT\n+GCAGTACTGTGCAAACTGAAATTTGGATTTTCGTAATGATCTGGTCCTGA\n+ATCTGTCATGTAGTCCGTACTCATATAAGTCGGATGCTCTTGGAAACGCA\n+TTTGATTTAATTGATGTTGTTGATTTAAAGTACTTCCAATTGACCCCGTA\n+TCATATGGCCTTTGGTACATAGGCTCCTGTAGCTGATATTCACAAGGACG\n+AGCGTTTGAAGTTGTAGCTGTTGTTGGTCCCATAGAATTAAGGGCGTAAC\n+TGTCATCATAAATAAGTTTTCCTGTCCGCATTGTGTATGTATGAAGATTC\n+GTATTTGCATTGCAAACAGCTGGGTAGTCAGTTTCAAAATGCTCCTGACT\n+AGAGCTTGATGTGCACGGAAGGAAAAAATTTGTCACATTTGAGTTATGGG\n+TGCCTGTGCCGTTTCCGACATGTTTTTCTCTGATTGCATTGTTAGGTGTA\n+CCACCATCTTGGCCATATGCACCCATACCAGAACCAATCATGCGAACATC\n+TCCAGCAACGGCACTCAAAGAATCGTGCTCGACACTTGTCTTTAGTCCAG\n+CTACCCAGGACATTAAAGTAATTATAGCTATCTCTATCAGACGCAGAGAG\n+AACTGATATCCCCATTGCAGCCAGTCGACATCGACAATACTTGTATGACG\n+ACATGAAATATATATAGCACCGAATATCTGAAGGGCTGCCAATAGTACAA\n+ACAATAGAGCTGTGGCAATCGTAATGTGAATGGCGTAAGACAAATTTTGA\n+TAGCCATGTATGTAGTTTTGAGATTTGCTGCGAAGAATGCGTTTTAAAAT\n+GCGGTATATGTAAAGATATAGCAGCCCTAGGCTCAGGCATATAAAAATAT\n+AAATTATCTGACATATTAAAGTTAATACCCGGGGCGGTGGTGGCAAAATT\n+GCCGATGGAGACATTGTAGCCGTAGGCTGGCCTTGTTGGTTATAAAGTTG\n+CTGCCGACGAAAGTACTGCTGTTGCTGCTGTTGTTGAAAGTATAAGTGAT\n'

diff -r 000000000000 -r f80c9e6700ba test-data/chr4_part.oascii.counts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chr4_part.oascii.counts Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,33532 @@\n+##windowmasker-statistics-format-version:oascii 1.0.0\n+##windowmasker-statistics-algorithm-version:1.0.0\n+##parameters:unit=8 t_low=8 t_high=52\n+AAAA\n+8\n+754 15 0 2\n+8\n+24\n+34\n+52\n+2\n+10\n+121\n+209\n+18\n+69\n+45\n+121\n+26\n+0\n+73\n+149\n+34\n+85\n+129\n+209\n+42\n+69\n+0\n+125\n+50\n+41\n+0\n+53\n+33\n+0\n+0\n+45\n+73\n+0\n+61\n+85\n+125\n+0\n+33\n+69\n+58\n+0\n+0\n+0\n+66\n+33\n+0\n+41\n+74\n+33\n+89\n+97\n+82\n+90\n+77\n+209\n+98\n+0\n+37\n+81\n+106\n+49\n+61\n+181\n+114\n+122\n+141\n+209\n+130\n+138\n+77\n+97\n+61\n+0\n+0\n+57\n+146\n+0\n+0\n+45\n+117\n+37\n+37\n+125\n+65\n+33\n+0\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+61\n+154\n+0\n+0\n+0\n+41\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+45\n+37\n+0\n+37\n+65\n+0\n+33\n+69\n+37\n+0\n+0\n+0\n+162\n+65\n+33\n+53\n+85\n+0\n+41\n+81\n+170\n+0\n+65\n+53\n+16777253\n+0\n+0\n+0\n+49\n+0\n+0\n+0\n+33\n+41\n+33\n+73\n+178\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+65\n+0\n+0\n+57\n+81\n+0\n+0\n+49\n+41\n+0\n+0\n+0\n+0\n+0\n+0\n+49\n+53\n+0\n+0\n+33\n+186\n+41\n+0\n+121\n+0\n+0\n+0\n+0\n+0\n+0\n+53\n+121\n+85\n+16777249\n+53\n+145\n+194\n+61\n+101\n+209\n+202\n+45\n+0\n+49\n+81\n+33\n+0\n+77\n+210\n+218\n+121\n+209\n+226\n+0\n+0\n+69\n+45\n+0\n+0\n+0\n+234\n+0\n+0\n+57\n+73\n+0\n+57\n+101\n+97\n+53\n+41\n+81\n+73\n+0\n+33\n+37\n+61\n+0\n+0\n+57\n+242\n+33\n+73\n+193\n+250\n+49\n+45\n+173\n+258\n+33\n+61\n+49\n+266\n+81\n+49\n+133\n+274\n+282\n+101\n+209\n+290\n+69\n+45\n+73\n+61\n+0\n+0\n+61\n+81\n+0\n+0\n+37\n+298\n+37\n+0\n+113\n+0\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+57\n+0\n+0\n+0\n+41\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+45\n+97\n+0\n+33\n+69\n+33\n+0\n+0\n+37\n+0\n+0\n+0\n+0\n+49\n+37\n+0\n+149\n+69\n+37\n+0\n+41\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+45\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+41\n+0\n+0\n+0\n+89\n+0\n+0\n+45\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+53\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+0\n+0\n+0\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+73\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+0\n+0\n+0\n+306\n+0\n+0\n+53\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+0\n+57\n+0\n+0\n+0\n+41\n+53\n+0\n+0\n+0\n+33\n+0\n+0\n+33\n+0\n+41\n+37\n+53\n+49\n+0\n+81\n+0\n+33\n+0\n+0\n+37\n+0\n+41\n+0\n+16777257\n+41\n+0\n+0\n+314\n+16777257\n+45\n+69\n+33\n+0\n+0\n+33\n+322\n+0\n+0\n+37\n+330\n+0\n+0\n+61\n+45\n+0\n+0\n+45\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+49\n+33\n+0\n+0\n+0\n+16777249\n+0\n+0\n+0\n+41\n+0\n+0\n+57\n+73\n+33\n+37\n+45\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+49\n+0\n+0\n+0\n+41\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+61\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+81\n+61\n+0\n+41\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+45\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+41\n+0\n+0\n+37\n+33\n+0\n+0\n+45\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+338\n+33\n+49\n+57\n+41\n+0\n+0\n+41\n+0\n+0\n+0\n+0\n+37\n+0\n+93\n+65\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+0\n+37\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+61\n+33\n+0\n+81\n+65\n+69\n+45\n+0\n+85\n+33\n+33\n+0\n+33\n+0\n+0\n+0\n+45\n+69\n+0\n+53\n+0\n+346\n+37\n+49\n+209\n+354\n+0\n+33\n+45\n+362\n+0\n+0\n+61\n+370\n+37\n+101\n+201\n+69\n+33\n+0\n+109\n+37\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+65\n+0\n+0\n+69\n+73\n+0\n+0\n+45\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+37\n+45\n+0\n+0\n+69\n+378\n+386\n+49\n+209\n+73\n+45\n+45\n+0\n+85\n+49\n+0\n+109\n+394\n+73\n+65\n+209\n+117\n+33\n+33\n+101\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+49\n+41\n+0\n+45\n+45\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+41\n+37\n+37\n+65\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+37\n+0\n+73\n+0\n+33\n+65\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+57\n+37\n+37\n+33\n+0\n+402\n+37\n+0\n+53\n+41\n+0\n+0\n+37\n+45\n+0\n+0\n+0\n+0\n+0\n+37\n+65\n+49\n+0\n+41\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+16777257\n+0\n+0\n+53\n+410\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+41\n+109\n+57\n+33\n+133\n+0\n+0\n+0\n+0\n+37\n+33\n+37\n+0\n+113\n+57\n+81\n+0\n+418\n+0\n+49\n+153\n+53\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+426\n+41\n+85\n+185\n+77\n+37\n+0\n+45\n+0\n+0\n+0\n+37\n+53\n+0\n+0\n+53\n+41\n+37\n+45\n+69\n+33\n+0\n+0\n+105\n+41\n+0\n+0\n+57\n+33\n+0\n+0\n+33\n+434\n+45\n+49\n+109\n+442\n+117\n+57\n+197\n+109\n+16777261\n+49\n+109\n+450\n+16777253\n+45\n+105\n+458\n+93\n+97\n+0\n+466\n+69\n+41\n+109\n+474\n+0\n+0\n+57\n+0\n+0\n+0\n+61\n+77\n+49\n+41\n+53\n+482\n+0\n+49\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+49\n+53\n+0\n+45\n+53\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0'..b'0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+57\n+0\n+0\n+0\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+37\n+0\n+0\n+53\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+37\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+49\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+33\n+0\n+0\n+0\n+125\n+33\n+0\n+0\n+37\n+41\n+0\n+0\n+0\n+0\n+0\n+0\n+97\n+0\n+0\n+0\n+77\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+81\n+0\n+0\n+0\n+33\n+0\n+0\n+0\n+0\n+0\n+0\n+0\n+41\n+0\n+0\n+0\n+85\n+37\n+0\n+0\n+37\n+0\n+0\n+0\n+33\n+45\n+0\n+0\n+89\n+57\n+0\n+0\n+539\n+52\n+523\n+39\n+524\n+39\n+523\n+25\n+525\n+52\n+533\n+37\n+522\n+17\n+520\n+10\n+521\n+17\n+528\n+24\n+535\n+52\n+521\n+18\n+525\n+21\n+522\n+28\n+529\n+52\n+522\n+24\n+524\n+37\n+521\n+17\n+521\n+15\n+523\n+16\n+520\n+9\n+522\n+29\n+520\n+22\n+523\n+23\n+532\n+52\n+521\n+23\n+527\n+52\n+522\n+23\n+526\n+29\n+520\n+10\n+522\n+35\n+523\n+52\n+520\n+18\n+525\n+18\n+541\n+52\n+526\n+16\n+528\n+35\n+520\n+21\n+525\n+15\n+522\n+31\n+520\n+13\n+520\n+19\n+522\n+22\n+530\n+52\n+524\n+15\n+520\n+17\n+529\n+52\n+529\n+52\n+522\n+15\n+521\n+52\n+521\n+18\n+520\n+19\n+529\n+52\n+522\n+35\n+520\n+24\n+523\n+52\n+522\n+20\n+521\n+52\n+523\n+34\n+520\n+10\n+520\n+15\n+520\n+9\n+521\n+18\n+521\n+16\n+520\n+15\n+523\n+10\n+524\n+22\n+520\n+11\n+521\n+15\n+521\n+16\n+522\n+8\n+525\n+52\n+520\n+31\n+521\n+52\n+522\n+52\n+525\n+20\n+526\n+15\n+523\n+51\n+526\n+52\n+521\n+8\n+526\n+46\n+520\n+8\n+522\n+41\n+522\n+19\n+522\n+9\n+520\n+12\n+522\n+21\n+520\n+16\n+520\n+9\n+528\n+52\n+520\n+9\n+524\n+31\n+521\n+31\n+520\n+18\n+520\n+36\n+520\n+12\n+522\n+17\n+531\n+52\n+520\n+13\n+523\n+18\n+522\n+14\n+533\n+52\n+520\n+16\n+522\n+23\n+521\n+11\n+520\n+26\n+529\n+44\n+531\n+30\n+520\n+13\n+521\n+27\n+521\n+24\n+520\n+26\n+520\n+21\n+529\n+8\n+523\n+12\n+521\n+10\n+521\n+24\n+521\n+11\n+525\n+37\n+522\n+29\n+520\n+9\n+525\n+20\n+522\n+12\n+526\n+9\n+524\n+11\n+521\n+10\n+524\n+23\n+527\n+31\n+521\n+13\n+521\n+23\n+525\n+26\n+520\n+15\n+524\n+22\n+525\n+17\n+522\n+13\n+531\n+9\n+524\n+30\n+520\n+11\n+521\n+24\n+524\n+19\n+523\n+9\n+521\n+14\n+521\n+9\n+521\n+8\n+520\n+14\n+526\n+16\n+531\n+52\n+525\n+18\n+522\n+21\n+534\n+52\n+520\n+19\n+522\n+14\n+525\n+42\n+522\n+24\n+520\n+13\n+520\n+18\n+530\n+39\n+520\n+12\n+528\n+25\n+524\n+21\n+523\n+25\n+524\n+31\n+522\n+11\n+522\n+15\n+535\n+51\n+530\n+34\n+521\n+10\n+525\n+39\n+526\n+24\n+525\n+41\n+522\n+25\n+525\n+9\n+532\n+17\n+523\n+41\n+520\n+15\n+520\n+13\n+520\n+13\n+530\n+34\n+521\n+20\n+534\n+50\n+524\n+15\n+520\n+12\n+522\n+8\n+522\n+15\n+520\n+10\n+522\n+23\n+520\n+12\n+522\n+22\n+524\n+17\n+533\n+52\n+520\n+20\n+523\n+32\n+522\n+9\n+525\n+32\n+523\n+16\n+522\n+9\n+520\n+9\n+523\n+30\n+523\n+36\n+531\n+31\n+524\n+43\n+525\n+21\n+537\n+28\n+521\n+12\n+525\n+10\n+521\n+9\n+535\n+52\n+523\n+17\n+529\n+34\n+525\n+36\n+524\n+32\n+527\n+22\n+526\n+15\n+521\n+9\n+521\n+19\n+522\n+18\n+523\n+18\n+544\n+52\n+521\n+25\n+522\n+52\n+525\n+31\n+523\n+20\n+521\n+13\n+522\n+22\n+534\n+52\n+524\n+24\n+541\n+52\n+564\n+44\n+538\n+15\n+524\n+13\n+564\n+32\n+533\n+18\n+524\n+12\n+526\n+13\n+520\n+10\n+523\n+8\n+529\n+9\n+564\n+25\n+522\n+12\n+533\n+8\n+549\n+16\n+530\n+14\n+557\n+21\n+528\n+11\n+560\n+21\n+531\n+8\n+522\n+16\n+524\n+9\n+522\n+8\n+532\n+17\n+548\n+9\n+522\n+10\n+556\n+19\n+534\n+15\n+522\n+10\n+532\n+8\n+530\n+17\n+525\n+9\n+520\n+14\n+564\n+29\n+530\n+13\n+559\n+19\n+529\n+12\n+521\n+8\n+539\n+15\n+550\n+14\n+520\n+8\n+525\n+11\n+531\n+9\n+524\n+9\n+539\n+18\n+528\n+8\n+536\n+8\n+557\n+18\n+524\n+8\n+531\n+14\n+535\n+9\n+521\n+9\n+533\n+11\n+540\n+8\n+550\n+8\n+542\n+13\n+520\n+10\n+529\n+8\n+520\n+8\n+525\n+10\n+526\n+11\n+521\n+9\n+526\n+15\n+530\n+11\n+522\n+9\n+527\n+11\n+523\n+12\n+564\n+17\n+529\n+9\n+549\n+19\n+556\n+11\n+534\n+9\n+520\n+12\n+564\n+35\n+526\n+12\n+544\n+25\n+541\n+18\n+531\n+9\n+564\n+17\n+545\n+15\n+520\n+8\n+528\n+15\n+531\n+13\n+562\n+28\n+564\n+12\n+530\n+9\n+541\n+10\n+529\n+10\n+528\n+10\n+520\n+10\n+558\n+14\n+525\n+14\n+526\n+8\n+521\n+9\n+564\n+32\n+541\n+11\n+523\n+11\n+533\n+36\n+526\n+11\n+530\n+8\n+525\n+11\n+535\n+10\n+521\n+11\n+525\n+13\n+523\n+18\n+524\n+11\n+521\n+10\n+528\n+11\n+530\n+17\n+521\n+8\n+526\n+15\n+520\n+8\n+532\n+8\n+523\n+12\n+537\n+15\n+527\n+9\n+528\n+11\n+522\n+8\n+522\n+8\n+530\n+9\n+530\n+11\n+522\n+10\n+539\n+13\n+520\n+11\n+524\n+8\n+538\n+8\n+524\n+10\n+532\n+8\n+540\n+17\n+564\n+24\n+554\n+14\n+530\n+8\n+528\n+9\n+521\n+10\n+555\n+16\n+540\n+11\n+520\n+9\n+558\n+21\n+522\n+9\n+521\n+8\n+534\n+14\n+558\n+14\n+527\n+10\n+538\n+11\n+545\n+11\n+535\n+9\n+564\n+22\n+554\n+18\n+526\n+9\n+539\n+9\n+564\n+31\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.advanced_wm.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.advanced_wm.bed Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,229 @@\n+chr4:100000-150000\t218\t229\twm_0\n+chr4:100000-150000\t710\t717\twm_1\n+chr4:100000-150000\t1419\t1432\twm_2\n+chr4:100000-150000\t2070\t2120\twm_3\n+chr4:100000-150000\t2270\t2277\twm_4\n+chr4:100000-150000\t2521\t2528\twm_5\n+chr4:100000-150000\t2580\t2588\twm_6\n+chr4:100000-150000\t2953\t2960\twm_7\n+chr4:100000-150000\t3028\t3084\twm_8\n+chr4:100000-150000\t3181\t3199\twm_9\n+chr4:100000-150000\t3297\t3305\twm_10\n+chr4:100000-150000\t3391\t3398\twm_11\n+chr4:100000-150000\t4856\t4866\twm_12\n+chr4:100000-150000\t4919\t4927\twm_13\n+chr4:100000-150000\t5063\t5133\twm_14\n+chr4:100000-150000\t5273\t5306\twm_15\n+chr4:100000-150000\t5369\t5376\twm_16\n+chr4:100000-150000\t5689\t5756\twm_17\n+chr4:100000-150000\t5759\t5814\twm_18\n+chr4:100000-150000\t6008\t6020\twm_19\n+chr4:100000-150000\t6038\t6045\twm_20\n+chr4:100000-150000\t6327\t6335\twm_21\n+chr4:100000-150000\t6376\t6383\twm_22\n+chr4:100000-150000\t6568\t6576\twm_23\n+chr4:100000-150000\t6736\t6743\twm_24\n+chr4:100000-150000\t6882\t6889\twm_25\n+chr4:100000-150000\t7332\t7397\twm_26\n+chr4:100000-150000\t9744\t9881\twm_27\n+chr4:100000-150000\t10791\t10863\twm_28\n+chr4:100000-150000\t10970\t11022\twm_29\n+chr4:100000-150000\t11322\t11329\twm_30\n+chr4:100000-150000\t11570\t11665\twm_31\n+chr4:100000-150000\t12024\t12109\twm_32\n+chr4:100000-150000\t12384\t12392\twm_33\n+chr4:100000-150000\t12505\t12513\twm_34\n+chr4:100000-150000\t12613\t12622\twm_35\n+chr4:100000-150000\t12869\t12981\twm_36\n+chr4:100000-150000\t13543\t13550\twm_37\n+chr4:100000-150000\t13754\t13817\twm_38\n+chr4:100000-150000\t14416\t14464\twm_39\n+chr4:100000-150000\t14869\t14889\twm_40\n+chr4:100000-150000\t15014\t15023\twm_41\n+chr4:100000-150000\t15739\t15746\twm_42\n+chr4:100000-150000\t18178\t18185\twm_43\n+chr4:100000-150000\t19264\t19334\twm_44\n+chr4:100000-150000\t19519\t19527\twm_45\n+chr4:100000-150000\t20367\t20410\twm_46\n+chr4:100000-150000\t20769\t20778\twm_47\n+chr4:100000-150000\t20832\t20852\twm_48\n+chr4:100000-150000\t21311\t21319\twm_49\n+chr4:100000-150000\t22018\t22154\twm_50\n+chr4:100000-150000\t23000\t23008\twm_51\n+chr4:100000-150000\t23429\t23439\twm_52\n+chr4:100000-150000\t23922\t23931\twm_53\n+chr4:100000-150000\t24010\t24017\twm_54\n+chr4:100000-150000\t24249\t24264\twm_55\n+chr4:100000-150000\t24781\t24788\twm_56\n+chr4:100000-150000\t25299\t25306\twm_57\n+chr4:100000-150000\t25616\t25679\twm_58\n+chr4:100000-150000\t25739\t25755\twm_59\n+chr4:100000-150000\t25961\t25968\twm_60\n+chr4:100000-150000\t26606\t26614\twm_61\n+chr4:100000-150000\t26980\t26988\twm_62\n+chr4:100000-150000\t26990\t27003\twm_63\n+chr4:100000-150000\t27286\t27293\twm_64\n+chr4:100000-150000\t27370\t27436\twm_65\n+chr4:100000-150000\t28490\t28553\twm_66\n+chr4:100000-150000\t29451\t29460\twm_67\n+chr4:100000-150000\t30099\t30107\twm_68\n+chr4:100000-150000\t30231\t30239\twm_69\n+chr4:100000-150000\t30810\t30817\twm_70\n+chr4:100000-150000\t31011\t31026\twm_71\n+chr4:100000-150000\t31593\t31656\twm_72\n+chr4:100000-150000\t32181\t32188\twm_73\n+chr4:100000-150000\t32410\t32470\twm_74\n+chr4:100000-150000\t32626\t32634\twm_75\n+chr4:100000-150000\t32714\t32721\twm_76\n+chr4:100000-150000\t32918\t32991\twm_77\n+chr4:100000-150000\t33406\t33451\twm_78\n+chr4:100000-150000\t33726\t33734\twm_79\n+chr4:100000-150000\t34064\t34073\twm_80\n+chr4:100000-150000\t34159\t34166\twm_81\n+chr4:100000-150000\t34749\t34757\twm_82\n+chr4:100000-150000\t35002\t35011\twm_83\n+chr4:100000-150000\t35030\t35037\twm_84\n+chr4:100000-150000\t35200\t35285\twm_85\n+chr4:100000-150000\t35671\t35714\twm_86\n+chr4:100000-150000\t36528\t36535\twm_87\n+chr4:100000-150000\t37189\t37207\twm_88\n+chr4:100000-150000\t37378\t37388\twm_89\n+chr4:100000-150000\t38208\t38216\twm_90\n+chr4:100000-150000\t38640\t38647\twm_91\n+chr4:100000-150000\t38658\t38852\twm_92\n+chr4:100000-150000\t38864\t38871\twm_93\n+chr4:100000-150000\t39024\t39032\twm_94\n+chr4:100000-150000\t39675\t39732\twm_95\n+chr4:100000-150000\t39945\t40019\twm_96\n+chr4:100000-150000\t40083\t40090\twm_97\n+chr4:100000-150000\t40856\t40863\twm_98\n+chr4:100000-150000\t42132\t42145\twm_99\n+chr4:100000-150000\t42178\t42185\twm_100\n+chr4:100000-150000\t42911\t42918\twm_101\n+chr4:100000-150000\t43360\t43367\twm_102\n+chr4:100000-150000\t43753\t43800\twm_103\n+chr4:100000-150000\t45136\t45149\twm_104\n+chr4:100000-150000\t46750\t46771\twm_105\n+chr4:100000-1500'..b'300000-350000\t6345\t6363\twm_126\n+chr4:300000-350000\t7270\t7277\twm_127\n+chr4:300000-350000\t7420\t7442\twm_128\n+chr4:300000-350000\t8557\t8564\twm_129\n+chr4:300000-350000\t9490\t9530\twm_130\n+chr4:300000-350000\t9677\t9685\twm_131\n+chr4:300000-350000\t10621\t10628\twm_132\n+chr4:300000-350000\t10740\t10747\twm_133\n+chr4:300000-350000\t10908\t10956\twm_134\n+chr4:300000-350000\t12006\t12013\twm_135\n+chr4:300000-350000\t12361\t12413\twm_136\n+chr4:300000-350000\t13397\t13405\twm_137\n+chr4:300000-350000\t13709\t13717\twm_138\n+chr4:300000-350000\t14215\t14363\twm_139\n+chr4:300000-350000\t14431\t14446\twm_140\n+chr4:300000-350000\t15038\t15051\twm_141\n+chr4:300000-350000\t15408\t15415\twm_142\n+chr4:300000-350000\t15686\t15693\twm_143\n+chr4:300000-350000\t15714\t15779\twm_144\n+chr4:300000-350000\t15845\t15854\twm_145\n+chr4:300000-350000\t16201\t16212\twm_146\n+chr4:300000-350000\t16288\t16296\twm_147\n+chr4:300000-350000\t16776\t16783\twm_148\n+chr4:300000-350000\t16901\t16909\twm_149\n+chr4:300000-350000\t16975\t17023\twm_150\n+chr4:300000-350000\t17478\t17487\twm_151\n+chr4:300000-350000\t17494\t17501\twm_152\n+chr4:300000-350000\t18112\t18123\twm_153\n+chr4:300000-350000\t18160\t18167\twm_154\n+chr4:300000-350000\t18549\t18563\twm_155\n+chr4:300000-350000\t18737\t18809\twm_156\n+chr4:300000-350000\t18919\t18943\twm_157\n+chr4:300000-350000\t19872\t19963\twm_158\n+chr4:300000-350000\t20267\t20342\twm_159\n+chr4:300000-350000\t20508\t20559\twm_160\n+chr4:300000-350000\t20560\t20575\twm_161\n+chr4:300000-350000\t20676\t20749\twm_162\n+chr4:300000-350000\t21212\t21220\twm_163\n+chr4:300000-350000\t21329\t21515\twm_164\n+chr4:300000-350000\t21519\t21528\twm_165\n+chr4:300000-350000\t21544\t21611\twm_166\n+chr4:300000-350000\t21821\t21888\twm_167\n+chr4:300000-350000\t22263\t22273\twm_168\n+chr4:300000-350000\t24141\t24148\twm_169\n+chr4:300000-350000\t26323\t26330\twm_170\n+chr4:300000-350000\t27422\t27482\twm_171\n+chr4:300000-350000\t27497\t27507\twm_172\n+chr4:300000-350000\t27566\t27597\twm_173\n+chr4:300000-350000\t27666\t27674\twm_174\n+chr4:300000-350000\t27953\t28028\twm_175\n+chr4:300000-350000\t28211\t28218\twm_176\n+chr4:300000-350000\t28414\t28470\twm_177\n+chr4:300000-350000\t28999\t29007\twm_178\n+chr4:300000-350000\t29020\t29028\twm_179\n+chr4:300000-350000\t29104\t29111\twm_180\n+chr4:300000-350000\t29852\t29859\twm_181\n+chr4:300000-350000\t30120\t30127\twm_182\n+chr4:300000-350000\t31154\t31162\twm_183\n+chr4:300000-350000\t31376\t31383\twm_184\n+chr4:300000-350000\t32004\t32094\twm_185\n+chr4:300000-350000\t32135\t32188\twm_186\n+chr4:300000-350000\t32862\t32871\twm_187\n+chr4:300000-350000\t33006\t33019\twm_188\n+chr4:300000-350000\t33986\t33993\twm_189\n+chr4:300000-350000\t34602\t34686\twm_190\n+chr4:300000-350000\t35591\t35599\twm_191\n+chr4:300000-350000\t35700\t35708\twm_192\n+chr4:300000-350000\t35729\t35740\twm_193\n+chr4:300000-350000\t35848\t35861\twm_194\n+chr4:300000-350000\t36100\t36108\twm_195\n+chr4:300000-350000\t36140\t36149\twm_196\n+chr4:300000-350000\t36248\t36259\twm_197\n+chr4:300000-350000\t36550\t36557\twm_198\n+chr4:300000-350000\t37068\t37079\twm_199\n+chr4:300000-350000\t37106\t37113\twm_200\n+chr4:300000-350000\t37291\t37298\twm_201\n+chr4:300000-350000\t37426\t37450\twm_202\n+chr4:300000-350000\t37634\t37710\twm_203\n+chr4:300000-350000\t37987\t37995\twm_204\n+chr4:300000-350000\t38700\t38756\twm_205\n+chr4:300000-350000\t39317\t39324\twm_206\n+chr4:300000-350000\t39627\t39635\twm_207\n+chr4:300000-350000\t39794\t39802\twm_208\n+chr4:300000-350000\t39866\t39948\twm_209\n+chr4:300000-350000\t40540\t40562\twm_210\n+chr4:300000-350000\t41426\t41547\twm_211\n+chr4:300000-350000\t41639\t41646\twm_212\n+chr4:300000-350000\t42307\t42814\twm_213\n+chr4:300000-350000\t43061\t43093\twm_214\n+chr4:300000-350000\t43133\t43140\twm_215\n+chr4:300000-350000\t43771\t43782\twm_216\n+chr4:300000-350000\t45993\t46001\twm_217\n+chr4:300000-350000\t46178\t46185\twm_218\n+chr4:300000-350000\t46560\t46580\twm_219\n+chr4:300000-350000\t46610\t46618\twm_220\n+chr4:300000-350000\t46873\t46881\twm_221\n+chr4:300000-350000\t48061\t48069\twm_222\n+chr4:300000-350000\t48498\t48561\twm_223\n+chr4:300000-350000\t48659\t48669\twm_224\n+chr4:300000-350000\t48713\t48773\twm_225\n+chr4:300000-350000\t49174\t49239\twm_226\n+chr4:300000-350000\t49701\t49719\twm_227\n+chr4:300000-350000\t49957\t49964\twm_228\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fa Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,2002 @@\n+>chr4:100000-150000\n+TAAATTTTATATGGTCGCAAAGGTTTTCTTTATTACGTTGCAGACTTCAG\n+AAAAAAGTCAATATATAGTCAAAAATGGTATTAAAATGTTTAAGATGCAA\n+TGCAATAAGAGTTTAGCAAGAGAGAATGCTATAGTCAATTTTCCCGTTAC\n+TCAGTAAAATTGAGAGAGTGGAATTGCACAATTTTTCTGGGATATCAATA\n+GATATTGGTCAATAAAATAAAAAAAAAAATTGTTTAAAAGTGTGGGAGTG\n+GTGGGGCGTGACCAAAGCGTTTTCGGCAAATCGAGACAAGCCTAATAAAA\n+ATATGAAAAAATAACAAATTCAATTCAATCATTTTCAAACGGTTTGTGGG\n+CGAAAGTGTTTTGACACATTTTGACACACCAATTCGAACGCCCAAAACTG\n+CCACGCCCAGACTTTTAAAAAATGTATTAATATTTTTTCACATTTTATTA\n+GATTTGTAAATTGCCACGTTTGTAAAGATTTGTAAAAATTAGGCTGCGCT\n+AACTCTAAACGGCCATTTTTTCTCATTTCATTCCTAACATCTATCGATAT\n+CCCAGAAAAAATATGAAATTTCGCGTTCGCATTCACACTAGCTGAGTAAC\n+GGGTATCTGATAGTCGGGGAACTAGACTATAGCATTCTGTCTTGTTTTAT\n+TTATTTTATAAATAATAACTTTAAAGAATGTGTGCTTGTATTATTTTAAA\n+ATGTATTTTCTTTTTTTCAATTTATGTTTTAAATTACAAAAGTAACAACA\n+ATTCCAAGTCGCAGCTCTATTTTATTTATAAGTTAATATATTTATGAACT\n+TAATATTAATATTAAAATTGATTTCTTCCCGAAAATCGTGTTTTAGTACA\n+AGCACGCACTCATAGACACCAGATATATGCATTAGTACACCGAAACTACA\n+AGTACACCGCATACACACACAGTATTTTTTGACTTTATACTTTATATGAT\n+CGAATACGCTTCCTTCTGCCTGTGACATACTTTTCAACAAATCTAGTATA\n+CCCTTTTACTCTACGAGTAACGGGTATAAAAATGCGACCTGTTTAATGCA\n+AAATGGCTAAATCAATTTCTTGAAGCACGACGTGCGGACAGAAACCCCCA\n+AGAAAAGATATCTACTCTTACTTTTCACACGTGGCAAGCTAAATACTCTA\n+TTGACAATTATTCTACTAAAAGGTCATTTTTGAAATTTATTTATGTGATA\n+GTATTGTACATAGCGTTAAGGCAATGCAAAGCAAGAATTTTTACATGGTG\n+CCAATTGATCAACAATAATATTGATTTAAAGTTTAAGTGAAATTTACAAT\n+GCATGAGCATACGTGTGCACACATACAGTTGTCGGCTGTCACTGCTGGCT\n+GTAGAGCTCTCCGCTTTCTGGCACTTGAATAAAAGTTCGAGAGAGCTGGA\n+TCCAGTTCTTAACCCAGTCAAAAAAAAAAAAATAAATAAATATCACGTTA\n+GAGAGCCAGCAGTGCTGTAGCTTGTATTATGAACCTTAAACGGCTAAGGA\n+TACCTGTATCGTCGGCAAATGTGGATGTGGATACTCTTAGGCAACTATTA\n+GGCGACGTTGCTGTATAGATGAGGTAAGAACTCTGCCTTGGGGGTGTTGC\n+ATCGCACTGCAAACTTTCTGGACGACTTAAGAATGTTCTGAGTTTTTACT\n+TTAAACATTAGGTCGTCGAGTCAGACTCTGTCGAATGCTTGGGATACGTC\n+TAAAAATACGGCTGTGTAGTACTCACGATTTTCGTATGCAGATCTTAGTT\n+TAGATTGTCGGGTTAGCAGGCATTTTTGAATACCTAACCAGACTTTGGAA\n+TCATTATGAAGATCGATCTTTTCCATCCTTCTGGGCAGAAACCAAGTTTG\n+GTGATGGTATTCAAGAGCTGAGTTATGTAGTGAACTGTAGAATGTGGGGC\n+AGCTCGATGATCATTTTTGGATCACATCTCAGCACATTTTTACGGGCTGA\n+GATTGTCTTTAACTAGACAGTTATTCCAATATAAAAATTTAGATTAGTAT\n+TACTAGAGACAATGCATTTATGTACATACACATATGTCCATAATTATTTG\n+CACGGTCGCAAGCCTCCCACTATTTTTTATTTTATTTATGTTAGGCATCT\n+ATGTATTTTAATTTTCTTTTGCAATCCCAATATCTAAGTAACTACCGAAA\n+CTATTGACGAAGTCGACTAAAACGGTGGAAAGACAATATTAAGTAACATA\n+AGTTTATTTGGGTATGTCCATATTGTGGCTTTGCCCACAGTCCGTAATAA\n+GTTTTAAATTTTGTAATAAATTTTTTTAGATAAAAATATATGTGCTCTCT\n+TCAGTTCAGTCAGAGGTTTCCAACGCAGTGAGAGGCATTTGTGACCATAT\n+GATGTATGTATTTTTAAGCAGTATGAACAAATCGATATATCCGTGACTTT\n+CTGGCCGTCCGTCTGTTTCTACTCATGATTTCATCATTATCGAACGACTA\n+TATAAAGTTAAAAGCTGTCATATGAACAATGTGAAAATTACTATCTAGTT\n+AGTTATTAAATAATGAATTGCTTTTTTTAATAAAACTACCTTTTTTATAG\n+CAATTAAATTGACACTTTCAAATAATACTGAAAAAAAATAATTAGTAAAA\n+AATTATCAGTATTAGGCATTTCACGTATATTAATTTTAAAGAGACAAATC\n+ATTCAATATTAAACTTTCATATTACATTACATACAATTTAAACATAGAAT\n+TACAATGCCTTCTAAAAATGTGCCGAACCAAATTATTATATAAAAGGATA\n+TCCCGTCACTTTTGAAACAACATTTACCGTAATACTGCAATTTTTACATC\n+TTGCGTGAATTTTGTTGATATAAACTGATAGATACTCTAATTAAAAAATG\n+ATTTTGCACCTGTTAGACCTATTATGAAATCGTCCACATTAAAAGACACT\n+GACCAAAAATCTCAGAACCACCCCCTTACATTTATCATACAATGATTAAG\n+TCCAAAAAAAGGACTACTATTATTAACTGCACGATATGCAACCCTATTTA\n+TCAATTTATAAGACCGAAAAACTCAAACTTTACTTATTATTTAGTTTTTA\n+TGTTTTTTAAATATTATTTATGCGTTTTAAATTTGTGGGAGGCACATTAA\n+ATCTAGTTGAAAATAAAATTATTATTTTCGTGGCACTAAAAATATTATTA\n+CAATGGCATGTAAAAACAAGAAAAAAGGCTCTATATATATATGGTATATC\n+CCTGAATATCAGATACCCGTTAATCACCTAGTGCAAACGCGAACGCGAAA\n+TTTCATCAGTTTTCGGGGATACCGATGGATATTGGGGAATAAATGAGAAA\n+AAAAATTAAAACTGTTCAAAAGTGTGGGCGTGACCTGTCGGTGGCACAAA\n+GTTTTTTGGTAAATCGATAGAAAATTTACAAGGTTAGAAAATTTTTTTAA\n+AAATATTAAAACGTTTTGCAAAAAAGGGCGTGGCAGTGATGGGCTGTATT\n+GGGGTTTTTTACAAATCGATAGAAATTTACAAGACTTCTTCTAGGTTTAA\n+TAGTTCCTGAGATCTCAGATCGACACGACTATTGATCCTGATCAAGAGTA\n+TATATACTTTATATGGTCGGAAACGCTTCCTTCTGCTTCAGTTACATACT\n+TTTCAACGAAACAAGTATACTCTTTTACTATACGAGTAACGGGTATAATT\n+ACAGTTCCTATTAATCAAGCCAAAATGTAGGCGCATGAACGTTTTATTTT\n+ATCTGGTGTTATTTGGTGTCCATGACCCTAAAAACAACACACTTCAAAAA\n+ACAAGCAGCAGTTTCGTTTTGTACTTTTCTAATTGGCAAGCAGATAAAAA\n+TATTAT'..b'GAAATATAACTCGAGCAGCAAAGCAAAAAAATATAAGTGCCACTAC\n+AACAATAAATCTAAAGGACCTGGAACGCTTTTGGGAATTGGAAGATGAAG\n+CCGATGAGACGATTAAAGACAATGCAGAATGAAACAACTGTCACCAACGA\n+GGAAGGCAGATTTGTGGTTGCAATTCCATTCCACAAAGAGGCATCGCCAA\n+ATAAAGGTTGCTGAGAAAAACCAAGAATACCAATATATCCTATGGAGAGA\n+TGATCCAAAATTGCCGATCAGTGAGTTTAAGTTAACAACCGTAACTTATG\n+GCACATCGGCAGCACCTTTCTTATCAGTCCGATGTCTACGAGAGTTGGCA\n+GATCTCTTTTGCCAAGGGGATAGCGTCTTACCAGAAAAAATGAGAGACGA\n+CTACTGGCCGTATATATATATATATATATAATTTTGGGTGTGCACGACAC\n+ACCATTTTCTAAAAAAAACAGATGAGGTTAGTAAGATGTACACTAGTGGG\n+CATAAGTATTTGGACAATAAATATTTTCAATATATTTGTTTGTAACTCAT\n+TGTTTACTTAAAGCAAAATTGTTTAATAATTTTAGTAAATAGGTAGACTA\n+TCGTAGTTAAATTAGGTAACATAAACATATGGATAACTTCATTGTTGATT\n+TAACAAAAATTACTTTCTTACAAATTAGCAGTGGCATAAGTATTTGGACA\n+AATTATTTAAATGTTATAAATTGAAAAAAAAGTCAACTACAAAATTATGA\n+TAAATTAATAAAAAATATAGCCTCCCTTAGCGTCTATCACCTTTTGCAGA\n+CGTTTTGGTACAGACTGTACCAAGCTGTGGATATAATCTATTGAAATATC\n+CTTCCATAAGGTTTGAATTTCCAAAATCGTTTCTTCGCGACTTCTAGATA\n+AGTTTGCACTCCTTTTTCTTTTTAAATATGACCAGAGGTTTTCTATTATG\n+TTGAGGTCTGGACTTTGAGGTGGCCAATCTAATGTGTTTATGCCAACATC\n+TTTCAGAAACTTCGTAATCAGTTTGGCCTTATGACAGGGAGCATTATCCT\n+GCTGGAGTATGAAGGACTCTCCAATCAATTTATCACCAGAGGGGAATGCA\n+TAATTATTAAGGACATCTAAATATTTTCTTTGATTCATGGTTCCATCAAC\n+AGGAACCAAATCTCCCAAGCCAGTGAAGGCTACACATCCCCAAAATCCCC\n+AGTTCCTCTGTTTTCACCATGTTTAACAAATTTATAACTGAAATAAATTG\n+TGATACGTAGTATCACGTTATCAAGAACCATTTGATCTAAAATACATAAG\n+TCAAAATTTTATATTCTTCGAACCAGAGATCAATGCGAAGTAATTAAATG\n+TGATGTCTAAATACTTTTGCCACCGCCCAAATCGTTGTCTGTCTAGCTTT\n+CTTATAAGCAGAAGGATAATTGAAAAGGTAAACGGCAAAACATACCTCTC\n+GCGTGTAACTGTAATTGCACTCTTTGTTTTATCATCAATAGTTTACTTAT\n+TTATTTGACTGTACTATGAAAAGCATAGCCTGGCAGTTGCAAGCTAATGG\n+TGTCTAAATACTTATGCCCACTAGTGTACTATCAAAATGGATTGTTTCTT\n+CGTTTGAGATTCAGATATGGTTTGCATCCAAATATTTCTTTTGCGGTGTG\n+CAAAGAGACTCCTATACAATCAAATATCTGCTATAGTGCAGTAGTACATT\n+TATATTTTTCTTGAAGGGTACTTTGATGACCTTTAAACTCAGCCGTACGG\n+TAATTATCGACCATAGTAGTAAATTCAAAAGAACGGAAAACCATTTTTCA\n+ATATGGTGGGCACCGCATCTTCTTGCCGTTTGTGGACGTTAAGAGGGCGT\n+AGTTATAGTGGCAGATAGATATTTTGTTGCATATAAATATAAATTTGCAA\n+GCAATTTGCCGAAAAAAAATTAGGATGAAAACTTGCTTATACAGGCTCCA\n+CTACACATGTATATCATCCTGCTATATTATCCAGCACCTTTAAACTCCAA\n+ATCCTGGGATACTTCAAAAATTCTTAAATTCCCACATCGACACGCCGACA\n+AAGCATTATCAAAGCATTTTCATATAACCATTGGCTTTTCTAAAGATTAT\n+AATAAAATAGCCTTATACTCCCTTATTCACGAGCTTAAAACTGGAATAAT\n+AGACATATGTAATAAACTTAATATTAGCGTTTACCAATAAAATCTATCCT\n+AATAAAAACCACAATTAGAAAATTATTAATTAAGCACCAAAACCAATTAT\n+CAAAAAGCAATATTTCAAGAGTATATTTGTTCGGCAGATAAATAAAAAAG\n+CTTCTGACCCTGTCGGCGTCTATATTCAAAATTTCTCGTAGTCAAAACAA\n+ATTCCCATTAACTAATATTTACTAAATTAATTAATTAACCAAAATAAACA\n+TTTTTAAATTATGTACATAGGAACCTTTTTTAAATACGTAACATCACTTC\n+CACTGGAGATTAACTTAAAGGTAACTTATTGTATCTTACCCTTTAACAAT\n+TTTAATTAGTTTTTTTTTTATATTTAAGGGCGACCTAATAATATGCATAT\n+ATTTGTAAATTCGAAAAAGAAAAACTTATAAACGTTGGTTTATTTAAAAA\n+ATATACATGCATTTTTTATAAAAGTTAATAAGTGTTAAGTCTATAGCAAT\n+CCGAAGTTGTTAAAGACATATTGAAATTTAACTTAGCCAGACACTAGATC\n+TTAATGTGGTAAACCATTAATTAGTTATTCATTTTACAAATACTAACGTC\n+AAAAAACTTATGCAATCGAAATTGAAAGATCTTAAGCCAATGAACATACA\n+TAAGCTGGTATATATAATCGTAATAACGTTAAACATTTACTCACGATAAT\n+ATCTTAGGTAATTTTCTTGTAGGTACTGAGGTAATCAGTTGTCCCCAGAC\n+AAGTGTACCAATTCCAAAAAATATACACCATAGCCACTGATCCAATGTTA\n+AAGCCTTCGTCGAGAAAGCCATTTTACCATATTGGATGATTAGCACCTTA\n+AATGTTGTGAAAATATTTTAAATGTATATATATGTGCATATGAATAACAT\n+TATATAGCATACCTGTGATATCATAGTGAATATCCATATGGTGTAAAATA\n+TGGGATTTGTAAGTAGGCCTTCAATGACATTGCGCTGCCCATGGATTTTT\n+CTAGCGTTTATTTCATTAAACAAAGTCATCATGACAAAAGTATTAAAGAT\n+AATAGTAAAGTGCTGTGTTGGTCCCGCGTTTAGTTCTTGTCCACGTCCAG\n+ATTCAATATCGAGTATAACATCGCCTTAAGCATAACAATTTTTTATTACA\n+AAGAAAGCATTGATTATGAATATAACTTACCGACAAATAACAATCCGAAT\n+ATTATTATTAACTGATACAGCGCCTGACCCAATATGTTCTTCATCATTGT\n+GCGGGAAATTAAAGGTTTTGTACGGCCATAGGGTTTGCGGAGCAATAGAT\n+CTGGTGTAGGAAACTCAGTTGCTAATGCAAGTGATGCCAATGTATCCATT\n+ATTAAGTTCACCCACAACATTTGCACTGCCTGAAATTTTGCTGTTATTAG\n+ATTTTTTCTTTTTTCTTTTAGTAACTTACTTTAAGCGGTGAATCTTGCAC\n+AGCACACGCACCAATAAATGCAACAATTACAGCGACTACATTTACTGTTA\n+ACTGAAACTGTAAAAACTTAGCAATAGAGTCATATACGTTGCGTCCCCAC\n+ATTACAGCTTTAACAATGCTGCTAAAATTATCGTCAGTTAATATTATATC\n+GGAAGCTTCTTTGGCAACATCTGTTCCGGCTATACCCATAGCAAATCCTA\n+CATCGGCTTTTTTTAAAGCTGGACCATCATTTGTGCCGTCTCCAGTTACA\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.interval Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,744 @@\n+>chr4:100000-150000\n+0 - 13\n+77 - 90\n+208 - 234\n+290 - 314\n+409 - 450\n+479 - 490\n+552 - 566\n+641 - 669\n+686 - 736\n+765 - 820\n+1022 - 1034\n+1180 - 1195\n+1260 - 1271\n+1416 - 1444\n+1975 - 1992\n+2068 - 2119\n+2248 - 2292\n+2355 - 2366\n+2501 - 2514\n+2519 - 2536\n+2578 - 2606\n+2625 - 2641\n+2728 - 2744\n+2836 - 2851\n+2953 - 2959\n+3028 - 3085\n+3106 - 3129\n+3134 - 3151\n+3179 - 3198\n+3295 - 3312\n+3385 - 3412\n+3689 - 3703\n+3791 - 3808\n+3863 - 3877\n+3916 - 3950\n+3968 - 4001\n+4011 - 4024\n+4399 - 4412\n+4466 - 4477\n+4546 - 4558\n+4626 - 4640\n+4701 - 4717\n+4826 - 4874\n+4913 - 4931\n+5063 - 5132\n+5163 - 5176\n+5217 - 5235\n+5269 - 5305\n+5366 - 5379\n+5411 - 5428\n+5479 - 5491\n+5685 - 5813\n+6005 - 6022\n+6038 - 6044\n+6115 - 6127\n+6325 - 6341\n+6370 - 6392\n+6441 - 6454\n+6506 - 6526\n+6558 - 6588\n+6668 - 6684\n+6732 - 6745\n+6879 - 6895\n+6919 - 6944\n+6985 - 7000\n+7286 - 7298\n+7332 - 7396\n+7997 - 8009\n+8067 - 8080\n+8126 - 8138\n+8170 - 8186\n+8523 - 8537\n+8546 - 8569\n+8576 - 8590\n+8835 - 8857\n+8877 - 8889\n+8906 - 8927\n+9162 - 9196\n+9365 - 9386\n+9472 - 9488\n+9544 - 9559\n+9593 - 9609\n+9624 - 9648\n+9744 - 9880\n+10084 - 10097\n+10155 - 10173\n+10180 - 10193\n+10229 - 10241\n+10358 - 10371\n+10465 - 10483\n+10506 - 10527\n+10591 - 10605\n+10612 - 10623\n+10654 - 10672\n+10733 - 10746\n+10789 - 10864\n+10913 - 10935\n+10968 - 11023\n+11047 - 11062\n+11114 - 11140\n+11176 - 11194\n+11305 - 11332\n+11443 - 11455\n+11477 - 11491\n+11567 - 11664\n+11775 - 11787\n+11953 - 11968\n+12024 - 12108\n+12129 - 12140\n+12158 - 12171\n+12279 - 12295\n+12380 - 12394\n+12424 - 12441\n+12502 - 12518\n+12533 - 12551\n+12595 - 12627\n+12658 - 12673\n+12767 - 12816\n+12869 - 12984\n+12995 - 13011\n+13119 - 13131\n+13223 - 13241\n+13245 - 13259\n+13298 - 13309\n+13543 - 13549\n+13556 - 13590\n+13724 - 13738\n+13753 - 13816\n+13827 - 13840\n+13868 - 13885\n+14071 - 14084\n+14230 - 14244\n+14309 - 14323\n+14416 - 14463\n+14523 - 14541\n+14863 - 14912\n+15012 - 15025\n+15052 - 15067\n+15736 - 15748\n+15764 - 15777\n+15986 - 16001\n+16117 - 16130\n+16242 - 16256\n+16398 - 16412\n+16450 - 16466\n+16509 - 16523\n+16546 - 16559\n+16634 - 16657\n+16790 - 16805\n+16825 - 16841\n+16944 - 16956\n+17372 - 17383\n+17642 - 17657\n+18174 - 18187\n+18436 - 18448\n+18508 - 18522\n+18937 - 18950\n+19263 - 19333\n+19355 - 19383\n+19387 - 19400\n+19495 - 19531\n+19542 - 19560\n+19576 - 19590\n+19667 - 19679\n+19698 - 19715\n+19845 - 19859\n+20262 - 20276\n+20367 - 20409\n+20727 - 20740\n+20764 - 20780\n+20797 - 20811\n+20830 - 20853\n+20987 - 21000\n+21254 - 21267\n+21306 - 21321\n+21374 - 21388\n+21692 - 21708\n+21798 - 21832\n+21929 - 21941\n+21965 - 21989\n+22015 - 22156\n+22286 - 22302\n+22996 - 23009\n+23248 - 23262\n+23421 - 23441\n+23449 - 23462\n+23744 - 23761\n+23901 - 23949\n+24004 - 24022\n+24148 - 24162\n+24230 - 24267\n+24781 - 24787\n+24958 - 24971\n+25299 - 25305\n+25614 - 25680\n+25735 - 25761\n+25961 - 25967\n+26597 - 26616\n+26642 - 26656\n+26818 - 26837\n+26977 - 27002\n+27116 - 27132\n+27170 - 27182\n+27225 - 27239\n+27263 - 27277\n+27283 - 27298\n+27305 - 27319\n+27370 - 27435\n+27443 - 27456\n+27497 - 27508\n+27516 - 27530\n+27697 - 27710\n+27739 - 27753\n+27796 - 27847\n+28121 - 28132\n+28239 - 28252\n+28385 - 28396\n+28490 - 28553\n+28748 - 28763\n+29027 - 29061\n+29076 - 29090\n+29133 - 29169\n+29235 - 29246\n+29309 - 29320\n+29423 - 29437\n+29442 - 29478\n+29529 - 29541\n+29566 - 29578\n+29596 - 29609\n+29654 - 29668\n+29849 - 29861\n+29938 - 29957\n+29988 - 30001\n+30092 - 30111\n+30228 - 30251\n+30305 - 30319\n+30343 - 30355\n+30491 - 30506\n+30549 - 30565\n+30695 - 30716\n+30781 - 30797\n+30807 - 30824\n+30887 - 30899\n+30947 - 30968\n+31008 - 31027\n+31051 - 31076\n+31156 - 31168\n+31342 - 31355\n+31469 - 31488\n+31593 - 31661\n+31785 - 31800\n+31812 - 31839\n+31854 - 31868\n+31966 - 31981\n+32084 - 32097\n+32175 - 32190\n+32314 - 32334\n+32369 - 32381\n+32403 - 32470\n+32519 - 32533\n+32537 - 32550\n+32619 - 32637\n+32709 - 32723\n+32863 - 32877\n+32916 - 32991\n+33079 - 33093\n+33105 - 33119\n+33139 - 33163\n+33230 - 33245\n+33404 - 33452\n+33482 - 33495\n+33530 - 33544\n+33685 - 33702\n+33722 - 33737\n+33759 - 33777\n+34059 - 34075\n+34098 - 3411'..b' - 14764\n+14937 - 14949\n+15034 - 15056\n+15093 - 15118\n+15130 - 15141\n+15221 - 15236\n+15373 - 15385\n+15404 - 15420\n+15458 - 15470\n+15683 - 15697\n+15714 - 15782\n+15843 - 15867\n+16196 - 16213\n+16281 - 16297\n+16306 - 16321\n+16359 - 16370\n+16426 - 16438\n+16605 - 16624\n+16649 - 16666\n+16739 - 16753\n+16772 - 16787\n+16807 - 16821\n+16863 - 16876\n+16901 - 16908\n+16971 - 17024\n+17164 - 17178\n+17475 - 17506\n+17567 - 17579\n+18037 - 18050\n+18104 - 18127\n+18155 - 18169\n+18518 - 18534\n+18546 - 18565\n+18584 - 18605\n+18638 - 18663\n+18676 - 18689\n+18694 - 18707\n+18735 - 18808\n+18869 - 18887\n+18919 - 18973\n+19066 - 19081\n+19363 - 19380\n+19801 - 19812\n+19872 - 19962\n+20076 - 20088\n+20267 - 20341\n+20508 - 20578\n+20676 - 20748\n+21115 - 21129\n+21191 - 21203\n+21209 - 21226\n+21329 - 21529\n+21537 - 21614\n+21819 - 21887\n+22059 - 22073\n+22250 - 22275\n+22330 - 22344\n+22574 - 22594\n+22649 - 22663\n+23005 - 23021\n+23937 - 23949\n+23978 - 23992\n+24054 - 24070\n+24135 - 24151\n+24201 - 24217\n+24385 - 24396\n+24545 - 24559\n+24622 - 24641\n+25202 - 25217\n+25322 - 25334\n+26022 - 26034\n+26317 - 26354\n+26476 - 26490\n+26706 - 26719\n+27419 - 27483\n+27495 - 27515\n+27562 - 27600\n+27653 - 27687\n+27762 - 27774\n+27953 - 28027\n+28159 - 28176\n+28211 - 28248\n+28355 - 28370\n+28414 - 28469\n+28692 - 28703\n+28798 - 28810\n+28844 - 28861\n+28949 - 28983\n+28995 - 29043\n+29102 - 29121\n+29171 - 29186\n+29200 - 29212\n+29537 - 29550\n+29592 - 29607\n+29738 - 29753\n+29813 - 29826\n+29852 - 29872\n+29887 - 29900\n+29969 - 30004\n+30028 - 30040\n+30114 - 30131\n+30205 - 30233\n+30381 - 30392\n+30423 - 30438\n+30484 - 30500\n+30507 - 30522\n+30550 - 30564\n+30587 - 30598\n+30661 - 30673\n+30734 - 30764\n+30843 - 30855\n+30901 - 30930\n+30962 - 30974\n+31149 - 31164\n+31201 - 31215\n+31271 - 31283\n+31331 - 31347\n+31373 - 31387\n+31435 - 31452\n+31861 - 31872\n+32004 - 32195\n+32308 - 32326\n+32470 - 32490\n+32747 - 32761\n+32844 - 32873\n+32906 - 32928\n+33000 - 33025\n+33238 - 33255\n+33288 - 33300\n+33476 - 33503\n+33694 - 33709\n+33817 - 33834\n+33857 - 33870\n+33968 - 33996\n+34048 - 34062\n+34257 - 34273\n+34313 - 34339\n+34549 - 34565\n+34602 - 34685\n+34722 - 34762\n+34830 - 34844\n+34906 - 34921\n+34986 - 34999\n+35017 - 35030\n+35081 - 35096\n+35131 - 35146\n+35165 - 35181\n+35194 - 35214\n+35282 - 35294\n+35408 - 35423\n+35461 - 35476\n+35549 - 35562\n+35587 - 35599\n+35694 - 35710\n+35726 - 35742\n+35844 - 35863\n+35924 - 35939\n+36095 - 36110\n+36137 - 36150\n+36242 - 36271\n+36428 - 36447\n+36471 - 36484\n+36544 - 36559\n+36615 - 36628\n+36758 - 36774\n+36780 - 36793\n+36940 - 36954\n+36992 - 37018\n+37042 - 37061\n+37065 - 37081\n+37106 - 37112\n+37249 - 37268\n+37288 - 37304\n+37320 - 37337\n+37420 - 37462\n+37631 - 37709\n+37748 - 37785\n+37796 - 37807\n+37841 - 37854\n+37982 - 37998\n+38032 - 38049\n+38075 - 38088\n+38276 - 38288\n+38320 - 38347\n+38399 - 38415\n+38454 - 38469\n+38554 - 38587\n+38697 - 38755\n+38777 - 38790\n+38851 - 38867\n+38932 - 38959\n+39115 - 39127\n+39293 - 39309\n+39317 - 39323\n+39484 - 39497\n+39573 - 39590\n+39623 - 39637\n+39723 - 39742\n+39790 - 39803\n+39821 - 39834\n+39866 - 39949\n+40047 - 40058\n+40090 - 40103\n+40110 - 40124\n+40175 - 40205\n+40230 - 40241\n+40247 - 40260\n+40312 - 40329\n+40453 - 40464\n+40532 - 40570\n+40845 - 40859\n+41124 - 41138\n+41190 - 41203\n+41225 - 41238\n+41402 - 41414\n+41424 - 41547\n+41637 - 41648\n+41700 - 41712\n+41882 - 41896\n+41975 - 41987\n+42012 - 42025\n+42053 - 42066\n+42165 - 42179\n+42189 - 42209\n+42307 - 42813\n+42815 - 42828\n+43059 - 43101\n+43128 - 43141\n+43188 - 43203\n+43329 - 43355\n+43451 - 43466\n+43667 - 43681\n+43765 - 43785\n+43841 - 43855\n+44069 - 44083\n+45289 - 45302\n+45990 - 46006\n+46091 - 46104\n+46175 - 46191\n+46558 - 46584\n+46607 - 46620\n+46663 - 46680\n+46720 - 46734\n+46848 - 46862\n+46871 - 46882\n+46899 - 46920\n+47066 - 47080\n+47266 - 47279\n+47450 - 47467\n+47644 - 47657\n+47845 - 47860\n+48029 - 48046\n+48059 - 48073\n+48245 - 48260\n+48367 - 48381\n+48436 - 48450\n+48498 - 48563\n+48573 - 48587\n+48644 - 48677\n+48713 - 48773\n+49062 - 49076\n+49156 - 49238\n+49433 - 49449\n+49496 - 49511\n+49701 - 49718\n+49887 - 49898\n+49955 - 49968\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.nodust_wm.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.nodust_wm.bed Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,754 @@\n+chr4:100000-150000\t0\t14\twm_0\n+chr4:100000-150000\t77\t91\twm_1\n+chr4:100000-150000\t208\t235\twm_2\n+chr4:100000-150000\t290\t315\twm_3\n+chr4:100000-150000\t409\t451\twm_4\n+chr4:100000-150000\t479\t491\twm_5\n+chr4:100000-150000\t552\t567\twm_6\n+chr4:100000-150000\t641\t670\twm_7\n+chr4:100000-150000\t686\t737\twm_8\n+chr4:100000-150000\t765\t821\twm_9\n+chr4:100000-150000\t1022\t1035\twm_10\n+chr4:100000-150000\t1180\t1196\twm_11\n+chr4:100000-150000\t1260\t1272\twm_12\n+chr4:100000-150000\t1416\t1445\twm_13\n+chr4:100000-150000\t1975\t1993\twm_14\n+chr4:100000-150000\t2068\t2091\twm_15\n+chr4:100000-150000\t2100\t2117\twm_16\n+chr4:100000-150000\t2248\t2293\twm_17\n+chr4:100000-150000\t2355\t2367\twm_18\n+chr4:100000-150000\t2501\t2515\twm_19\n+chr4:100000-150000\t2519\t2537\twm_20\n+chr4:100000-150000\t2578\t2607\twm_21\n+chr4:100000-150000\t2625\t2642\twm_22\n+chr4:100000-150000\t2728\t2745\twm_23\n+chr4:100000-150000\t2836\t2852\twm_24\n+chr4:100000-150000\t3031\t3086\twm_25\n+chr4:100000-150000\t3106\t3130\twm_26\n+chr4:100000-150000\t3134\t3152\twm_27\n+chr4:100000-150000\t3179\t3194\twm_28\n+chr4:100000-150000\t3295\t3313\twm_29\n+chr4:100000-150000\t3385\t3413\twm_30\n+chr4:100000-150000\t3689\t3704\twm_31\n+chr4:100000-150000\t3791\t3809\twm_32\n+chr4:100000-150000\t3863\t3878\twm_33\n+chr4:100000-150000\t3916\t3951\twm_34\n+chr4:100000-150000\t3968\t4002\twm_35\n+chr4:100000-150000\t4011\t4025\twm_36\n+chr4:100000-150000\t4399\t4413\twm_37\n+chr4:100000-150000\t4466\t4478\twm_38\n+chr4:100000-150000\t4546\t4559\twm_39\n+chr4:100000-150000\t4626\t4641\twm_40\n+chr4:100000-150000\t4701\t4718\twm_41\n+chr4:100000-150000\t4826\t4875\twm_42\n+chr4:100000-150000\t4913\t4932\twm_43\n+chr4:100000-150000\t5079\t5115\twm_44\n+chr4:100000-150000\t5163\t5177\twm_45\n+chr4:100000-150000\t5217\t5236\twm_46\n+chr4:100000-150000\t5269\t5284\twm_47\n+chr4:100000-150000\t5288\t5303\twm_48\n+chr4:100000-150000\t5366\t5380\twm_49\n+chr4:100000-150000\t5411\t5429\twm_50\n+chr4:100000-150000\t5479\t5492\twm_51\n+chr4:100000-150000\t5685\t5760\twm_52\n+chr4:100000-150000\t5780\t5802\twm_53\n+chr4:100000-150000\t6005\t6023\twm_54\n+chr4:100000-150000\t6115\t6128\twm_55\n+chr4:100000-150000\t6325\t6342\twm_56\n+chr4:100000-150000\t6370\t6393\twm_57\n+chr4:100000-150000\t6441\t6455\twm_58\n+chr4:100000-150000\t6506\t6527\twm_59\n+chr4:100000-150000\t6558\t6589\twm_60\n+chr4:100000-150000\t6668\t6685\twm_61\n+chr4:100000-150000\t6732\t6746\twm_62\n+chr4:100000-150000\t6879\t6896\twm_63\n+chr4:100000-150000\t6919\t6945\twm_64\n+chr4:100000-150000\t6985\t7001\twm_65\n+chr4:100000-150000\t7286\t7299\twm_66\n+chr4:100000-150000\t7339\t7371\twm_67\n+chr4:100000-150000\t7997\t8010\twm_68\n+chr4:100000-150000\t8067\t8081\twm_69\n+chr4:100000-150000\t8126\t8139\twm_70\n+chr4:100000-150000\t8170\t8187\twm_71\n+chr4:100000-150000\t8523\t8538\twm_72\n+chr4:100000-150000\t8546\t8570\twm_73\n+chr4:100000-150000\t8576\t8591\twm_74\n+chr4:100000-150000\t8835\t8858\twm_75\n+chr4:100000-150000\t8877\t8890\twm_76\n+chr4:100000-150000\t8906\t8928\twm_77\n+chr4:100000-150000\t9162\t9197\twm_78\n+chr4:100000-150000\t9365\t9387\twm_79\n+chr4:100000-150000\t9472\t9489\twm_80\n+chr4:100000-150000\t9544\t9560\twm_81\n+chr4:100000-150000\t9593\t9610\twm_82\n+chr4:100000-150000\t9624\t9649\twm_83\n+chr4:100000-150000\t9756\t9776\twm_84\n+chr4:100000-150000\t9782\t9833\twm_85\n+chr4:100000-150000\t9837\t9851\twm_86\n+chr4:100000-150000\t10084\t10098\twm_87\n+chr4:100000-150000\t10155\t10174\twm_88\n+chr4:100000-150000\t10180\t10194\twm_89\n+chr4:100000-150000\t10229\t10242\twm_90\n+chr4:100000-150000\t10358\t10372\twm_91\n+chr4:100000-150000\t10465\t10484\twm_92\n+chr4:100000-150000\t10506\t10528\twm_93\n+chr4:100000-150000\t10591\t10606\twm_94\n+chr4:100000-150000\t10612\t10624\twm_95\n+chr4:100000-150000\t10654\t10673\twm_96\n+chr4:100000-150000\t10733\t10747\twm_97\n+chr4:100000-150000\t10789\t10823\twm_98\n+chr4:100000-150000\t10852\t10865\twm_99\n+chr4:100000-150000\t10913\t10936\twm_100\n+chr4:100000-150000\t10968\t10988\twm_101\n+chr4:100000-150000\t11003\t11024\twm_102\n+chr4:100000-150000\t11047\t11063\twm_103\n+chr4:100000-150000\t11114\t11141\twm_104\n+chr4:100000-150000\t11176\t11195\twm_105\n+chr4:100000-150000\t11305\t11333\twm_106\n+chr4:100000-150000\t11443\t11456\twm_107\n+chr4:100000-150000\t11477\t11492\twm_108\n+chr4:100000-150000\t11567\t11593\twm_109\n'..b'0\t37249\t37269\twm_651\n+chr4:300000-350000\t37288\t37305\twm_652\n+chr4:300000-350000\t37320\t37338\twm_653\n+chr4:300000-350000\t37420\t37463\twm_654\n+chr4:300000-350000\t37631\t37679\twm_655\n+chr4:300000-350000\t37684\t37703\twm_656\n+chr4:300000-350000\t37748\t37786\twm_657\n+chr4:300000-350000\t37796\t37808\twm_658\n+chr4:300000-350000\t37841\t37855\twm_659\n+chr4:300000-350000\t37982\t37999\twm_660\n+chr4:300000-350000\t38032\t38050\twm_661\n+chr4:300000-350000\t38075\t38089\twm_662\n+chr4:300000-350000\t38276\t38289\twm_663\n+chr4:300000-350000\t38320\t38348\twm_664\n+chr4:300000-350000\t38399\t38416\twm_665\n+chr4:300000-350000\t38454\t38470\twm_666\n+chr4:300000-350000\t38554\t38588\twm_667\n+chr4:300000-350000\t38697\t38745\twm_668\n+chr4:300000-350000\t38777\t38791\twm_669\n+chr4:300000-350000\t38851\t38868\twm_670\n+chr4:300000-350000\t38932\t38960\twm_671\n+chr4:300000-350000\t39115\t39128\twm_672\n+chr4:300000-350000\t39293\t39310\twm_673\n+chr4:300000-350000\t39484\t39498\twm_674\n+chr4:300000-350000\t39573\t39591\twm_675\n+chr4:300000-350000\t39623\t39638\twm_676\n+chr4:300000-350000\t39723\t39743\twm_677\n+chr4:300000-350000\t39790\t39804\twm_678\n+chr4:300000-350000\t39821\t39835\twm_679\n+chr4:300000-350000\t39884\t39921\twm_680\n+chr4:300000-350000\t39935\t39950\twm_681\n+chr4:300000-350000\t40047\t40059\twm_682\n+chr4:300000-350000\t40090\t40104\twm_683\n+chr4:300000-350000\t40110\t40125\twm_684\n+chr4:300000-350000\t40175\t40206\twm_685\n+chr4:300000-350000\t40230\t40242\twm_686\n+chr4:300000-350000\t40247\t40261\twm_687\n+chr4:300000-350000\t40312\t40330\twm_688\n+chr4:300000-350000\t40453\t40465\twm_689\n+chr4:300000-350000\t40532\t40571\twm_690\n+chr4:300000-350000\t40845\t40860\twm_691\n+chr4:300000-350000\t41124\t41139\twm_692\n+chr4:300000-350000\t41190\t41204\twm_693\n+chr4:300000-350000\t41225\t41239\twm_694\n+chr4:300000-350000\t41402\t41415\twm_695\n+chr4:300000-350000\t41424\t41548\twm_696\n+chr4:300000-350000\t41637\t41649\twm_697\n+chr4:300000-350000\t41700\t41713\twm_698\n+chr4:300000-350000\t41882\t41897\twm_699\n+chr4:300000-350000\t41975\t41988\twm_700\n+chr4:300000-350000\t42012\t42026\twm_701\n+chr4:300000-350000\t42053\t42067\twm_702\n+chr4:300000-350000\t42165\t42180\twm_703\n+chr4:300000-350000\t42189\t42210\twm_704\n+chr4:300000-350000\t42317\t42436\twm_705\n+chr4:300000-350000\t42457\t42485\twm_706\n+chr4:300000-350000\t42499\t42547\twm_707\n+chr4:300000-350000\t42557\t42612\twm_708\n+chr4:300000-350000\t42641\t42719\twm_709\n+chr4:300000-350000\t42732\t42747\twm_710\n+chr4:300000-350000\t42777\t42799\twm_711\n+chr4:300000-350000\t42815\t42829\twm_712\n+chr4:300000-350000\t43059\t43102\twm_713\n+chr4:300000-350000\t43128\t43142\twm_714\n+chr4:300000-350000\t43188\t43204\twm_715\n+chr4:300000-350000\t43329\t43356\twm_716\n+chr4:300000-350000\t43451\t43467\twm_717\n+chr4:300000-350000\t43667\t43682\twm_718\n+chr4:300000-350000\t43765\t43786\twm_719\n+chr4:300000-350000\t43841\t43856\twm_720\n+chr4:300000-350000\t44069\t44084\twm_721\n+chr4:300000-350000\t45289\t45303\twm_722\n+chr4:300000-350000\t45990\t46007\twm_723\n+chr4:300000-350000\t46091\t46105\twm_724\n+chr4:300000-350000\t46175\t46192\twm_725\n+chr4:300000-350000\t46558\t46585\twm_726\n+chr4:300000-350000\t46607\t46621\twm_727\n+chr4:300000-350000\t46663\t46681\twm_728\n+chr4:300000-350000\t46720\t46735\twm_729\n+chr4:300000-350000\t46848\t46863\twm_730\n+chr4:300000-350000\t46871\t46883\twm_731\n+chr4:300000-350000\t46899\t46921\twm_732\n+chr4:300000-350000\t47066\t47081\twm_733\n+chr4:300000-350000\t47266\t47280\twm_734\n+chr4:300000-350000\t47450\t47468\twm_735\n+chr4:300000-350000\t47644\t47658\twm_736\n+chr4:300000-350000\t47845\t47861\twm_737\n+chr4:300000-350000\t48029\t48047\twm_738\n+chr4:300000-350000\t48059\t48074\twm_739\n+chr4:300000-350000\t48245\t48261\twm_740\n+chr4:300000-350000\t48367\t48382\twm_741\n+chr4:300000-350000\t48436\t48451\twm_742\n+chr4:300000-350000\t48522\t48536\twm_743\n+chr4:300000-350000\t48544\t48564\twm_744\n+chr4:300000-350000\t48573\t48588\twm_745\n+chr4:300000-350000\t48644\t48678\twm_746\n+chr4:300000-350000\t48737\t48774\twm_747\n+chr4:300000-350000\t49062\t49077\twm_748\n+chr4:300000-350000\t49156\t49185\twm_749\n+chr4:300000-350000\t49433\t49450\twm_750\n+chr4:300000-350000\t49496\t49512\twm_751\n+chr4:300000-350000\t49887\t49899\twm_752\n+chr4:300000-350000\t49955\t49969\twm_753\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.seqid_wm.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.seqid_wm.bed Tue May 16 13:18:12 2017 -0400

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.wm.asn1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.wm.asn1 Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,3724 @@\n+Blast-db-mask-info ::= {\n+ algo-id 3,\n+ algo-program windowmasker,\n+ algo-options "",\n+ masks {\n+ masks {\n+ packed-int {\n+ {\n+ from 0,\n+ to 13,\n+ id local id 1\n+ },\n+ {\n+ from 77,\n+ to 90,\n+ id local id 1\n+ },\n+ {\n+ from 208,\n+ to 234,\n+ id local id 1\n+ },\n+ {\n+ from 290,\n+ to 314,\n+ id local id 1\n+ },\n+ {\n+ from 409,\n+ to 450,\n+ id local id 1\n+ },\n+ {\n+ from 479,\n+ to 490,\n+ id local id 1\n+ },\n+ {\n+ from 552,\n+ to 566,\n+ id local id 1\n+ },\n+ {\n+ from 641,\n+ to 669,\n+ id local id 1\n+ },\n+ {\n+ from 686,\n+ to 736,\n+ id local id 1\n+ },\n+ {\n+ from 765,\n+ to 820,\n+ id local id 1\n+ },\n+ {\n+ from 1022,\n+ to 1034,\n+ id local id 1\n+ },\n+ {\n+ from 1180,\n+ to 1195,\n+ id local id 1\n+ },\n+ {\n+ from 1260,\n+ to 1271,\n+ id local id 1\n+ },\n+ {\n+ from 1416,\n+ to 1444,\n+ id local id 1\n+ },\n+ {\n+ from 1975,\n+ to 1992,\n+ id local id 1\n+ },\n+ {\n+ from 2068,\n+ to 2119,\n+ id local id 1\n+ },\n+ {\n+ from 2248,\n+ to 2292,\n+ id local id 1\n+ },\n+ {\n+ from 2355,\n+ to 2366,\n+ id local id 1\n+ },\n+ {\n+ from 2501,\n+ to 2514,\n+ id local id 1\n+ },\n+ {\n+ from 2519,\n+ to 2536,\n+ id local id 1\n+ },\n+ {\n+ from 2578,\n+ to 2606,\n+ id local id 1\n+ },\n+ {\n+ from 2625,\n+ to 2641,\n+ id local id 1\n+ },\n+ {\n+ from 2728,\n+ to 2744,\n+ id local id 1\n+ },\n+ {\n+ from 2836,\n+ to 2851,\n+ id local id 1\n+ },\n+ {\n+ from 2953,\n+ to 2959,\n+ id local id 1\n+ },\n+ {\n+ from 3028,\n+ to 3085,\n+ id local id 1\n+ },\n+ {\n+ from 3106,\n+ to 3129,\n+ id local id 1\n+ },\n+ {\n+ from 3134,\n+ to 3151,\n+ id local id 1\n+ },\n+ {\n+ from 3179,\n+ to 3198,\n+ id local id 1\n+ },\n+ {\n+ from 3295,\n+ to 3312,\n+ id local id 1\n+ },\n+ {\n+ from 3385,\n+ to 3412,\n+ id local id 1\n+ },\n+ {\n+ from 3689,\n+ to 3703,\n+ id local id 1\n+ },\n+ {\n+ from 3791,\n+ to 3808,\n+ id local id 1\n+ },\n+ {\n+ from 3863,\n+ to 3877,\n+ id local id 1\n+ },\n+ {\n+ from 3916,\n+ to 3950,\n+ id local id 1\n+ },\n+ {\n+ from 3968,\n+ to 4001,\n+ id local id 1\n+ },\n+ {\n+ from 4011,\n+ to 4024,\n+ id local id 1\n+ },\n+ {\n+ from 4399,\n+ to 4412,\n+ id local id 1\n+ },\n+ {\n+ from 4466,\n+ to 4477,\n+ id local id 1\n+ },\n+ {\n+ from 4546,\n+ to 4558,\n+ id local id 1\n+ },\n+ {\n+ from 4626,\n+ to 4640,\n+ id local id 1\n+ },\n+ {\n+ from 4701,\n+ to 4717,\n+ id local id 1\n+ },\n+ {\n+ from 4826,\n+ to 4874,\n+ id local id 1\n+ },\n+'..b'},\n+ {\n+ from 42307,\n+ to 42813,\n+ id local id 2\n+ },\n+ {\n+ from 42815,\n+ to 42828,\n+ id local id 2\n+ },\n+ {\n+ from 43059,\n+ to 43101,\n+ id local id 2\n+ },\n+ {\n+ from 43128,\n+ to 43141,\n+ id local id 2\n+ },\n+ {\n+ from 43188,\n+ to 43203,\n+ id local id 2\n+ },\n+ {\n+ from 43329,\n+ to 43355,\n+ id local id 2\n+ },\n+ {\n+ from 43451,\n+ to 43466,\n+ id local id 2\n+ },\n+ {\n+ from 43667,\n+ to 43681,\n+ id local id 2\n+ },\n+ {\n+ from 43765,\n+ to 43785,\n+ id local id 2\n+ },\n+ {\n+ from 43841,\n+ to 43855,\n+ id local id 2\n+ },\n+ {\n+ from 44069,\n+ to 44083,\n+ id local id 2\n+ },\n+ {\n+ from 45289,\n+ to 45302,\n+ id local id 2\n+ },\n+ {\n+ from 45990,\n+ to 46006,\n+ id local id 2\n+ },\n+ {\n+ from 46091,\n+ to 46104,\n+ id local id 2\n+ },\n+ {\n+ from 46175,\n+ to 46191,\n+ id local id 2\n+ },\n+ {\n+ from 46558,\n+ to 46584,\n+ id local id 2\n+ },\n+ {\n+ from 46607,\n+ to 46620,\n+ id local id 2\n+ },\n+ {\n+ from 46663,\n+ to 46680,\n+ id local id 2\n+ },\n+ {\n+ from 46720,\n+ to 46734,\n+ id local id 2\n+ },\n+ {\n+ from 46848,\n+ to 46862,\n+ id local id 2\n+ },\n+ {\n+ from 46871,\n+ to 46882,\n+ id local id 2\n+ },\n+ {\n+ from 46899,\n+ to 46920,\n+ id local id 2\n+ },\n+ {\n+ from 47066,\n+ to 47080,\n+ id local id 2\n+ },\n+ {\n+ from 47266,\n+ to 47279,\n+ id local id 2\n+ },\n+ {\n+ from 47450,\n+ to 47467,\n+ id local id 2\n+ },\n+ {\n+ from 47644,\n+ to 47657,\n+ id local id 2\n+ },\n+ {\n+ from 47845,\n+ to 47860,\n+ id local id 2\n+ },\n+ {\n+ from 48029,\n+ to 48046,\n+ id local id 2\n+ },\n+ {\n+ from 48059,\n+ to 48073,\n+ id local id 2\n+ },\n+ {\n+ from 48245,\n+ to 48260,\n+ id local id 2\n+ },\n+ {\n+ from 48367,\n+ to 48381,\n+ id local id 2\n+ },\n+ {\n+ from 48436,\n+ to 48450,\n+ id local id 2\n+ },\n+ {\n+ from 48498,\n+ to 48563,\n+ id local id 2\n+ },\n+ {\n+ from 48573,\n+ to 48587,\n+ id local id 2\n+ },\n+ {\n+ from 48644,\n+ to 48677,\n+ id local id 2\n+ },\n+ {\n+ from 48713,\n+ to 48773,\n+ id local id 2\n+ },\n+ {\n+ from 49062,\n+ to 49076,\n+ id local id 2\n+ },\n+ {\n+ from 49156,\n+ to 49238,\n+ id local id 2\n+ },\n+ {\n+ from 49433,\n+ to 49449,\n+ id local id 2\n+ },\n+ {\n+ from 49496,\n+ to 49511,\n+ id local id 2\n+ },\n+ {\n+ from 49701,\n+ to 49718,\n+ id local id 2\n+ },\n+ {\n+ from 49887,\n+ to 49898,\n+ id local id 2\n+ },\n+ {\n+ from 49955,\n+ to 49968,\n+ id local id 2\n+ }\n+ }\n+ },\n+ more FALSE\n+ }\n+}\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.wm.asnb

Binary file test-data/contigs.wm.asnb has changed

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.wm.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.wm.bed Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,742 @@\n+chr4:100000-150000\t0\t14\twm_0\n+chr4:100000-150000\t77\t91\twm_1\n+chr4:100000-150000\t208\t235\twm_2\n+chr4:100000-150000\t290\t315\twm_3\n+chr4:100000-150000\t409\t451\twm_4\n+chr4:100000-150000\t479\t491\twm_5\n+chr4:100000-150000\t552\t567\twm_6\n+chr4:100000-150000\t641\t670\twm_7\n+chr4:100000-150000\t686\t737\twm_8\n+chr4:100000-150000\t765\t821\twm_9\n+chr4:100000-150000\t1022\t1035\twm_10\n+chr4:100000-150000\t1180\t1196\twm_11\n+chr4:100000-150000\t1260\t1272\twm_12\n+chr4:100000-150000\t1416\t1445\twm_13\n+chr4:100000-150000\t1975\t1993\twm_14\n+chr4:100000-150000\t2068\t2120\twm_15\n+chr4:100000-150000\t2248\t2293\twm_16\n+chr4:100000-150000\t2355\t2367\twm_17\n+chr4:100000-150000\t2501\t2515\twm_18\n+chr4:100000-150000\t2519\t2537\twm_19\n+chr4:100000-150000\t2578\t2607\twm_20\n+chr4:100000-150000\t2625\t2642\twm_21\n+chr4:100000-150000\t2728\t2745\twm_22\n+chr4:100000-150000\t2836\t2852\twm_23\n+chr4:100000-150000\t2953\t2960\twm_24\n+chr4:100000-150000\t3028\t3086\twm_25\n+chr4:100000-150000\t3106\t3130\twm_26\n+chr4:100000-150000\t3134\t3152\twm_27\n+chr4:100000-150000\t3179\t3199\twm_28\n+chr4:100000-150000\t3295\t3313\twm_29\n+chr4:100000-150000\t3385\t3413\twm_30\n+chr4:100000-150000\t3689\t3704\twm_31\n+chr4:100000-150000\t3791\t3809\twm_32\n+chr4:100000-150000\t3863\t3878\twm_33\n+chr4:100000-150000\t3916\t3951\twm_34\n+chr4:100000-150000\t3968\t4002\twm_35\n+chr4:100000-150000\t4011\t4025\twm_36\n+chr4:100000-150000\t4399\t4413\twm_37\n+chr4:100000-150000\t4466\t4478\twm_38\n+chr4:100000-150000\t4546\t4559\twm_39\n+chr4:100000-150000\t4626\t4641\twm_40\n+chr4:100000-150000\t4701\t4718\twm_41\n+chr4:100000-150000\t4826\t4875\twm_42\n+chr4:100000-150000\t4913\t4932\twm_43\n+chr4:100000-150000\t5063\t5133\twm_44\n+chr4:100000-150000\t5163\t5177\twm_45\n+chr4:100000-150000\t5217\t5236\twm_46\n+chr4:100000-150000\t5269\t5306\twm_47\n+chr4:100000-150000\t5366\t5380\twm_48\n+chr4:100000-150000\t5411\t5429\twm_49\n+chr4:100000-150000\t5479\t5492\twm_50\n+chr4:100000-150000\t5685\t5814\twm_51\n+chr4:100000-150000\t6005\t6023\twm_52\n+chr4:100000-150000\t6038\t6045\twm_53\n+chr4:100000-150000\t6115\t6128\twm_54\n+chr4:100000-150000\t6325\t6342\twm_55\n+chr4:100000-150000\t6370\t6393\twm_56\n+chr4:100000-150000\t6441\t6455\twm_57\n+chr4:100000-150000\t6506\t6527\twm_58\n+chr4:100000-150000\t6558\t6589\twm_59\n+chr4:100000-150000\t6668\t6685\twm_60\n+chr4:100000-150000\t6732\t6746\twm_61\n+chr4:100000-150000\t6879\t6896\twm_62\n+chr4:100000-150000\t6919\t6945\twm_63\n+chr4:100000-150000\t6985\t7001\twm_64\n+chr4:100000-150000\t7286\t7299\twm_65\n+chr4:100000-150000\t7332\t7397\twm_66\n+chr4:100000-150000\t7997\t8010\twm_67\n+chr4:100000-150000\t8067\t8081\twm_68\n+chr4:100000-150000\t8126\t8139\twm_69\n+chr4:100000-150000\t8170\t8187\twm_70\n+chr4:100000-150000\t8523\t8538\twm_71\n+chr4:100000-150000\t8546\t8570\twm_72\n+chr4:100000-150000\t8576\t8591\twm_73\n+chr4:100000-150000\t8835\t8858\twm_74\n+chr4:100000-150000\t8877\t8890\twm_75\n+chr4:100000-150000\t8906\t8928\twm_76\n+chr4:100000-150000\t9162\t9197\twm_77\n+chr4:100000-150000\t9365\t9387\twm_78\n+chr4:100000-150000\t9472\t9489\twm_79\n+chr4:100000-150000\t9544\t9560\twm_80\n+chr4:100000-150000\t9593\t9610\twm_81\n+chr4:100000-150000\t9624\t9649\twm_82\n+chr4:100000-150000\t9744\t9881\twm_83\n+chr4:100000-150000\t10084\t10098\twm_84\n+chr4:100000-150000\t10155\t10174\twm_85\n+chr4:100000-150000\t10180\t10194\twm_86\n+chr4:100000-150000\t10229\t10242\twm_87\n+chr4:100000-150000\t10358\t10372\twm_88\n+chr4:100000-150000\t10465\t10484\twm_89\n+chr4:100000-150000\t10506\t10528\twm_90\n+chr4:100000-150000\t10591\t10606\twm_91\n+chr4:100000-150000\t10612\t10624\twm_92\n+chr4:100000-150000\t10654\t10673\twm_93\n+chr4:100000-150000\t10733\t10747\twm_94\n+chr4:100000-150000\t10789\t10865\twm_95\n+chr4:100000-150000\t10913\t10936\twm_96\n+chr4:100000-150000\t10968\t11024\twm_97\n+chr4:100000-150000\t11047\t11063\twm_98\n+chr4:100000-150000\t11114\t11141\twm_99\n+chr4:100000-150000\t11176\t11195\twm_100\n+chr4:100000-150000\t11305\t11333\twm_101\n+chr4:100000-150000\t11443\t11456\twm_102\n+chr4:100000-150000\t11477\t11492\twm_103\n+chr4:100000-150000\t11567\t11665\twm_104\n+chr4:100000-150000\t11775\t11788\twm_105\n+chr4:100000-150000\t11953\t11969\twm_106\n+chr4:100000-150000\t12024\t12109\twm_107\n+chr4:100000-150000\t12129\t12141\twm_108\n+chr4:100000-150000\t12158\t12172\tw'..b'0\t36758\t36775\twm_639\n+chr4:300000-350000\t36780\t36794\twm_640\n+chr4:300000-350000\t36940\t36955\twm_641\n+chr4:300000-350000\t36992\t37019\twm_642\n+chr4:300000-350000\t37042\t37062\twm_643\n+chr4:300000-350000\t37065\t37082\twm_644\n+chr4:300000-350000\t37106\t37113\twm_645\n+chr4:300000-350000\t37249\t37269\twm_646\n+chr4:300000-350000\t37288\t37305\twm_647\n+chr4:300000-350000\t37320\t37338\twm_648\n+chr4:300000-350000\t37420\t37463\twm_649\n+chr4:300000-350000\t37631\t37710\twm_650\n+chr4:300000-350000\t37748\t37786\twm_651\n+chr4:300000-350000\t37796\t37808\twm_652\n+chr4:300000-350000\t37841\t37855\twm_653\n+chr4:300000-350000\t37982\t37999\twm_654\n+chr4:300000-350000\t38032\t38050\twm_655\n+chr4:300000-350000\t38075\t38089\twm_656\n+chr4:300000-350000\t38276\t38289\twm_657\n+chr4:300000-350000\t38320\t38348\twm_658\n+chr4:300000-350000\t38399\t38416\twm_659\n+chr4:300000-350000\t38454\t38470\twm_660\n+chr4:300000-350000\t38554\t38588\twm_661\n+chr4:300000-350000\t38697\t38756\twm_662\n+chr4:300000-350000\t38777\t38791\twm_663\n+chr4:300000-350000\t38851\t38868\twm_664\n+chr4:300000-350000\t38932\t38960\twm_665\n+chr4:300000-350000\t39115\t39128\twm_666\n+chr4:300000-350000\t39293\t39310\twm_667\n+chr4:300000-350000\t39317\t39324\twm_668\n+chr4:300000-350000\t39484\t39498\twm_669\n+chr4:300000-350000\t39573\t39591\twm_670\n+chr4:300000-350000\t39623\t39638\twm_671\n+chr4:300000-350000\t39723\t39743\twm_672\n+chr4:300000-350000\t39790\t39804\twm_673\n+chr4:300000-350000\t39821\t39835\twm_674\n+chr4:300000-350000\t39866\t39950\twm_675\n+chr4:300000-350000\t40047\t40059\twm_676\n+chr4:300000-350000\t40090\t40104\twm_677\n+chr4:300000-350000\t40110\t40125\twm_678\n+chr4:300000-350000\t40175\t40206\twm_679\n+chr4:300000-350000\t40230\t40242\twm_680\n+chr4:300000-350000\t40247\t40261\twm_681\n+chr4:300000-350000\t40312\t40330\twm_682\n+chr4:300000-350000\t40453\t40465\twm_683\n+chr4:300000-350000\t40532\t40571\twm_684\n+chr4:300000-350000\t40845\t40860\twm_685\n+chr4:300000-350000\t41124\t41139\twm_686\n+chr4:300000-350000\t41190\t41204\twm_687\n+chr4:300000-350000\t41225\t41239\twm_688\n+chr4:300000-350000\t41402\t41415\twm_689\n+chr4:300000-350000\t41424\t41548\twm_690\n+chr4:300000-350000\t41637\t41649\twm_691\n+chr4:300000-350000\t41700\t41713\twm_692\n+chr4:300000-350000\t41882\t41897\twm_693\n+chr4:300000-350000\t41975\t41988\twm_694\n+chr4:300000-350000\t42012\t42026\twm_695\n+chr4:300000-350000\t42053\t42067\twm_696\n+chr4:300000-350000\t42165\t42180\twm_697\n+chr4:300000-350000\t42189\t42210\twm_698\n+chr4:300000-350000\t42307\t42814\twm_699\n+chr4:300000-350000\t42815\t42829\twm_700\n+chr4:300000-350000\t43059\t43102\twm_701\n+chr4:300000-350000\t43128\t43142\twm_702\n+chr4:300000-350000\t43188\t43204\twm_703\n+chr4:300000-350000\t43329\t43356\twm_704\n+chr4:300000-350000\t43451\t43467\twm_705\n+chr4:300000-350000\t43667\t43682\twm_706\n+chr4:300000-350000\t43765\t43786\twm_707\n+chr4:300000-350000\t43841\t43856\twm_708\n+chr4:300000-350000\t44069\t44084\twm_709\n+chr4:300000-350000\t45289\t45303\twm_710\n+chr4:300000-350000\t45990\t46007\twm_711\n+chr4:300000-350000\t46091\t46105\twm_712\n+chr4:300000-350000\t46175\t46192\twm_713\n+chr4:300000-350000\t46558\t46585\twm_714\n+chr4:300000-350000\t46607\t46621\twm_715\n+chr4:300000-350000\t46663\t46681\twm_716\n+chr4:300000-350000\t46720\t46735\twm_717\n+chr4:300000-350000\t46848\t46863\twm_718\n+chr4:300000-350000\t46871\t46883\twm_719\n+chr4:300000-350000\t46899\t46921\twm_720\n+chr4:300000-350000\t47066\t47081\twm_721\n+chr4:300000-350000\t47266\t47280\twm_722\n+chr4:300000-350000\t47450\t47468\twm_723\n+chr4:300000-350000\t47644\t47658\twm_724\n+chr4:300000-350000\t47845\t47861\twm_725\n+chr4:300000-350000\t48029\t48047\twm_726\n+chr4:300000-350000\t48059\t48074\twm_727\n+chr4:300000-350000\t48245\t48261\twm_728\n+chr4:300000-350000\t48367\t48382\twm_729\n+chr4:300000-350000\t48436\t48451\twm_730\n+chr4:300000-350000\t48498\t48564\twm_731\n+chr4:300000-350000\t48573\t48588\twm_732\n+chr4:300000-350000\t48644\t48678\twm_733\n+chr4:300000-350000\t48713\t48774\twm_734\n+chr4:300000-350000\t49062\t49077\twm_735\n+chr4:300000-350000\t49156\t49239\twm_736\n+chr4:300000-350000\t49433\t49450\twm_737\n+chr4:300000-350000\t49496\t49512\twm_738\n+chr4:300000-350000\t49701\t49719\twm_739\n+chr4:300000-350000\t49887\t49899\twm_740\n+chr4:300000-350000\t49955\t49969\twm_741\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.wm.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.wm.fa Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,1670 @@\n+>chr4:100000-150000\n+taaattttatatggTCGCAAAGGTTTTCTTTATTACGTTGCAGACTTCAGAAAAAAGTCA\n+ATATATAGTCAAAAATGgtattaaaatgtttAAGATGCAATGCAATAAGAGTTTAGCAAG\n+AGAGAATGCTATAGTCAATTTTCCCGTTACTCAGTAAAATTGAGAGAGTGGAATTGCACA\n+ATTTTTCTGGGATATCAATAGATATTGGtcaataaaataaaaaaaaaaattgtttAAAAG\n+TGTGGGAGTGGTGGGGCGTGACCAAAGCGTTTTCGGCAAATCGAGACAAGcctaataaaa\n+atatgaaaaaataacAAATTCAATTCAATCATTTTCAAACGGTTTGTGGGCGAAAGTGTT\n+TTGACACATTTTGACACACCAATTCGAACGCCCAAAACTGCCACGCCCAgacttttaaaa\n+aatgtattaatattttttcacattttattagATTTGTAAATTGCCACGTTTGTAAAGATt\n+tgtaaaaattaGGCTGCGCTAACTCTAAACGGCCATTTTTTCTCATTTCATTCCTAACAT\n+CTATCGATATCCcagaaaaaatatgaaATTTCGCGTTCGCATTCACACTAGCTGAGTAAC\n+GGGTATCTGATAGTCGGGGAACTAGACTATAGCATTCTGTCttgttttatttattttata\n+aataataactTTAAAGAATGTGTGCTtgtattattttaaaatgtattttctttttttcaa\n+tttatgttttaaattacAAAAGTAACAACAATTCCAAGTCGCAGCtctattttatttata\n+agttaatatatttatgaacttaatattaatattaaaattgaTTTCTTCCCGAAAATCGTG\n+TTTTAGTACAAGCACGCACTCATAGACACCAGATATATGCATTAGTACACCGAAACTACA\n+AGTACACCGCATACACACACAGTATTTTTTGACTTTATACTTTATATGATCGAATACGCT\n+TCCTTCTGCCTGTGACATACTTTTCAACAAATCTAGTATACCCTTTTACTCTACGAGTAA\n+CGggtataaaaatgcGACCTGTTTAATGCAAAATGGCTAAATCAATTTCTTGAAGCACGA\n+CGTGCGGACAGAAACCCCCAAGAAAAGATATCTACTCTTACTTTTCACACGTGGCAAGCT\n+AAATACTCTATTGACAATTATTCTACTAAAAGGTCATTTTtgaaatttatttatgtGATA\n+GTATTGTACATAGCGTTAAGGCAATGCAAAGCAAGAATTTTTACATGGTGCCAATTGATC\n+aacaataatattGATTTAAAGTTTAAGTGAAATTTACAATGCATGAGCATACGTGTGCAC\n+ACATACAGTTGTCGGCTGTCACTGCTGGCTGTAGAGCTCTCCGCTTTCTGGCACTTGAAT\n+AAAAGTTCGAGAGAGCTGGATCCAGTTCTTAACCCAgtcaaaaaaaaaaaaataaataaa\n+tatcaCGTTAGAGAGCCAGCAGTGCTGTAGCTTGTATTATGAACCTTAAACGGCTAAGGA\n+TACCTGTATCGTCGGCAAATGTGGATGTGGATACTCTTAGGCAACTATTAGGCGACGTTG\n+CTGTATAGATGAGGTAAGAACTCTGCCTTGGGGGTGTTGCATCGCACTGCAAACTTTCTG\n+GACGACTTAAGAATGTTCTGAGTTTTTACTTTAAACATTAGGTCGTCGAGTCAGACTCTG\n+TCGAATGCTTGGGATACGTCTAAAAATACGGCTGTGTAGTACTCACGATTTTCGTATGCA\n+GATCTTAGTTTAGATTGTCGGGTTAGCAGGCATTTTTGAATACCTAACCAGACTTTGGAA\n+TCATTATGAAGATCGATCTTTTCCATCCTTCTGGGCAGAAACCAAGTTTGGTGATGGTAT\n+TCAAGAGCTGAGTTATGTAGTGAACTGTAGAATGTGGGGCAGCTCGATGATCATTTTTGG\n+ATCACATCTCAGCACATTTTTACGGGCTGAGATTGTCTTTAACTAGACAGTTATTccaat\n+ataaaaatttagaTTAGTATTACTAGAGACAATGCATTTATGTACATACACATATGTCCA\n+TAATTATTTGCACGGTCGCAAGCCTCCCactattttttattttatttatgttaggcatct\n+atgtattttaattttcttttGCAATCCCAATATCTAAGTAACTACCGAAACTATTGACGA\n+AGTCGACTAAAACGGTGGAAAGACAATATTAAGTAACATAAGTTTATTTGGGTATGTCCA\n+TATTGTGGCTTTGCCCACAGTCCGTAATaagttttaaattttgtaataaatttttttaga\n+taaaaatatatgtGCTCTCTTCAGTTCAGTCAGAGGTTTCCAACGCAGTGAGAGGCATTT\n+GTGACCATATGATGTatgtatttttaaGCAGTATGAACAAATCGATATATCCGTGACTTT\n+CTGGCCGTCCGTCTGTTTCTACTCATGATTTCATCATTATCGAACGACTATATAAAGTTA\n+AAAGCTGTCATATGAACAATGTGAAAATTACTATCTAGTTAgttattaaataatgAATTg\n+ctttttttaataaaactACCTTTTTTATAGCAATTAAATTGACACTTTCAAATAATACtg\n+aaaaaaaataattagtaaaaaattatcAGTATTAGGCATTTCACGtatattaattttaaa\n+gaGACAAATCATTCAATATTAAACTTTCATATTACATTACATACAATTTAAACATAGAAT\n+TACAATGCCTTCTAAAAATGTGCCGAACcaaattattatataaaaGGATATCCCGTCACT\n+TTTGAAACAACATTTACCGTAATACTGCAATTTTTACATCTTGCGTGAATTTTGTTGATA\n+TAAACTGATAGATACTctaattaaaaaatgatTTTGCACCTGTTAGACCTATTATGAAAT\n+CGTCCACATTAAAAGACACTGACCAAAAATCTCAGAACCACCCCCTTACATTTATCATAC\n+AATGATTAAGTCCaaaaaaaGGACTACTATTATTAACTGCACGATATGCAACCCTATTTA\n+TCAATTTATAAGACCGAAAAACTCAAACtttacttattatttagtttttatgttttttaa\n+atattatttatgcgttttaaatttgtGGGAGGCACATTAAATCTAGttgaaaataaaatt\n+attattttcgTGGCactaaaaatattattacaATGGCATGTAAAAACAAGAAAAAAGGCt\n+ctatatatatatggtatatCCCTGAATATCAGATACCCGTTAATCACCTAGTGCAAACGC\n+GAACGCGAAATTTCATCAGTTTTCGGGGATACCGATGGATATTGGGGAATAAATGagaaa\n+aaaaattaaaactGTTCAAAAGTGTGGGCGTGACCTGTCGGTGGCACAAAGTTTTTTGGT\n+AAATCGATAGAAAATTTACAAGGTTagaaaatttttttaaaaatattaaaacgTTTTGCA\n+AAAAAGGGCGTGGCAGTGATGGGCTGTATTGGGGTTTTTTACAAATCGATAGAAATTTAC\n+AAGACTTCTTCTAGGTTTAATAGTTCCTGAGATCTCAGATCGACACGACTATTGATCCTG\n+ATCAAGAGTATATATACTTTATATGGTCGGAAACGCTTCCTTCTGCTTCAGTTACATACT\n+TTTCAACGAAACAAGTATACTCTTTTACTATACGAGTAACGGGTATAATTACAGTTCCTA\n+TTAATCAAGCCAAAATGTAGGCGCATGAAcgttttattttatctGGTGTTATTTGGTGTC\n+CATGACCCTAAAAACAACACACTTCAAAAAACAAGCAGCAGTTTCGTTTTGTACTTTTCT\n+AATTGGCAAGCagataaaaatattattccATCGTATTGTAGATGCATAGAGC'..b'AGCTTTGG\n+ATGGATTGTGTCCGGAAATATAACTCGAGCAGCAAagcaaaaaaatataagtGCCACTAC\n+AACAATAAATCTAAAGGACCTGGAACGCTTTTGGGAATTGGAAGATGAAGCCGATGAGAC\n+GATTAAAGACAATGCAGAATGAAACAACTGTCACCAACGAGGAAGGCAGATTTGTGGTTG\n+CAATTCCATTCCACAAAGAGGCATCGCCAAATAAAGGTTGCTGAGAAAAACCAAGAATAC\n+CAATATATCCTATGGAGAGATGATCCAAAATTGCCGATCAGTGAGTTTAAGTTAACAACC\n+GTAACTTATGGCACATCGGCAGCACCTTTCTTATCAGTCCGATGTCTACGAGAGTTGGCA\n+GATCTCTTTTGCCAAGGGGATAGCGTCTTACCAGAAAAAATGAGAGACGACTACTGGCcg\n+tatatatatatatatatataattttGGGTGTGCACGACACACCATTTtctaaaaaaaaca\n+gATGAGGTTAGTAAGATGTACACTAGTGGGCATAAGTATTTGGacaataaatattttcaa\n+tATATTTGTTTGTAACTCATTGTTTACTTAAAGCAAAATTgtttaataattttagTAAAT\n+AGGTAGACTATCGTAGTTAAATTAGGTAACATAAACATATGGATAACTTCATTGTTGATT\n+TAACAAAAATTACTTTCTTACAAATTAGCAGTGGCATAAGTATTTGGAcaaattatttaa\n+atgTTATAAATtgaaaaaaaagtCAACTACAAAATTATGataaattaataaaaaatatag\n+cCTCCCTTAGCGTCTATCACCTTTTGCAGACGTTTTGGTACAGACTGTACCAAGCTGTGG\n+ATATAATCTATTGAAATATCCTTCCATAAGGTTTGAATTTCCAAAATCGTTTCTTCGCGA\n+CTTCTAGATAAGTTTGCACTCCTTTTtctttttaaatatgaCCAGAGGTTTTCTATTATG\n+TTGAGGTCTGGACTTTGAGGTGGCCAATCTAATGTGTTTATGCCAACATCTTTCAGAAAC\n+TTCGTAATCAGTTTGGCCTTATGACAGGGAGCATTATCCTGCTGGAGTATGAAGGACTCT\n+CCAATCAATTTATCACCAGAGGGGAATGCATAATTATTAAGGACATctaaatattttctt\n+TGATTCATGGTTCCATCAACAGGAACCAAATCTCCCAAGCCAGTGAAGGCTACACATCCC\n+CAAAATCCCCAGTTCCTCTGTTTTCACCATGTTTAACAAATTTATAACTGAAATAAATTG\n+TGATACGTAGTATCACGTTATCAAGAACCATTTGATCTAAAATACATAAGtcaaaatttt\n+atattcttCGAACCAGAGATCAATGCGAAGTAATTAAATGTGATGTCTAAATACTTTTGC\n+CACCGCCCAAATCGTTGTCTGTCTAGCTTTCTTATAAGCAGAAGGATAATTGAAAAGGTA\n+AACGGCAAAACATACCTCTCGCGTGTAACTGTAATTGCACTCTTTGTTTTATCATCAATA\n+GTTTacttatttatttgaCTGTACTATGAAAAGCATAGCCTGGCAGTTGCAAGCTAATGG\n+TGTCTAAATACTTATGCCCACTAGTGTACTATCAAAATGGATTGTTTCTTCGTTTGAGAT\n+TCAGATATGGTTTGCATCCAAATATTTCTTTTGCGGTGTGCAAAGAGACTCCTATACAAT\n+CAAATATCTGCTATAGTGCAGTAGTacatttatatttttctTGAAGGGTACTTTGATGAC\n+CTTTAAACTCAGCCGTACGGTAATTATCGACCATAGTAGTAAATTCAAAAGAACGGAAAA\n+CCATTTTTCAATATGGTGGGCACCGCATCTTCTTGCCGTTTGTGGACGTTAAGAGGGCGT\n+AGTTATAGTGGCAGATAGATATTTTGTTGcatataaatataaatttgCAAGCAATTTGCc\n+gaaaaaaaattaggATGAAAACTTGCTTATACAGGCTCCACTACACATGTATATCATCCT\n+GCTATATTATCCAGCACCTTTAAACTCCAAATCCTGGGATACTTCAAAAATTCTTAAATT\n+CCCACATCGACACGCCGACAAAGCATTATCAAAGCATTTTCATATAACCATTGGCTTTTC\n+TAAAGattataataaaatagcCTTATACTCCCTTATTCACGAGCTTAAAACTGGAATAAT\n+AGACATATGTAATAAACTTAATATTAGCGTTTACCAATAAAATCTATCCTAATAAAAACC\n+ACAATTAgaaaattattaattaAGCACCAAAACCAATTATCAAAAAGCAATATTTCAAGA\n+GTATATTTGTTCGGCAgataaataaaaaagcTTCTGACCCTGTCGGCGTCTATATTCAAA\n+ATTTCTCGTAGTCAAAACaaattcccattaactaatatttactaaattaattaattaacc\n+aaaataaacatttttaaattatgtACATAGGAAccttttttaaatacgTAACATCACTTC\n+CACTGGAGATTAACTTAAAGGTAACTTATTGTATCTTACCCTTTaacaattttaattagt\n+tttttttttatatttaagGGCGACCTAATAATATGCATATATTTGTAAATTCGaaaaaga\n+aaaacttataaacgttggtttatttaaaaaatatacatgcattttttataaaagTTAATA\n+AGTGTTAAGTCTATAGCAATCCGAAGTTGTTAAAGACATATTGAAATTTAACTTAGCCAG\n+ACACTAGATCTTAATGTGGTAAACCATTAATTAGTTATTCATTTTACAAATACTAACGTC\n+AAAAAACTTATGCAATCGAAATTGAAAGATCTTAAGCCAATGAACATACATAAGCTGGTA\n+TATATAATCGTAATAACGTTAAACATTTACTCACGATAATATCTTAGGTAATTTTCTTGT\n+AGGTACTGAGGTAATCAGTTGTCCCCAGACAAGTGTACCAATtccaaaaaatatacaCCA\n+TAGCCACTGATCCAATGTTAAAGCCTTCGTCGAGAAAGCCATTTTACCATATTGGATGAT\n+TAGCACCTTAAATGTTgtgaaaatattttaaatgtatatatatgtgcatatgaataacat\n+tatatagcatacctgtgatatcatagtgaatatccatatGGTGTAAAATATGGGATTTGT\n+AAGTAGGCCTTCAATGACATTGCGCTGCCCATGGATTTTTCTAGCGTTTATTTCATTAAA\n+CAAAGTCATCATGACAAAAGTATTAAAGATAATAGTAAAGTGCTGTGTTGGTCCCGCGTT\n+TAGTTCTTGTCCACGTCCAGATTCAATATCGAGTATAACATCGCCTTAAGCATaacaatt\n+ttttattacaAAGAAAGCATTGATTATGAATATAACTTACCGACAAATAACAATCCgaat\n+attattattaacTGATACAGCGCCTGACCCAATATGTTCTTCATCATTGTGCGGGAAATT\n+AAAGGTTTTGTACGGCCATAGGGTTTGCGGAGCAATAGATCTGGTGTAGGAAACTCAGTT\n+GCTAATGCAAGTGATGCCAATGTATCCATTATTAAGTTCACCCACAACATTTGCACTGCC\n+TGAAATTTTGCTGTTATTAGAttttttcttttttcttttAGTAACTTACTTTAAGCGGTG\n+AATCTTGCACAGCACACGCACCAATAAATGCAACAATTACAGCGACTACATTTACTGTTA\n+ACTGAAACTGTAAAAACTTAGCAATAGAGTCATATACGTTGCGTCCCCACATTACAGCTT\n+TAACAATGCTGCTAAAATTATCGTCAGttaatattatatCGGAAGCTTCTTTGGCAACAT\n+CTGTTCCGGCTATACCCATAGCAAATCCTACATCGgctttttttaaagcTGGACCATCAT\n+TTGTGCCGTCTCCAGTTACA\n'

diff -r 000000000000 -r f80c9e6700ba test-data/contigs.wm.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.wm.xml Tue May 16 13:18:12 2017 -0400

b'@@ -0,0 +1,9674 @@\n+<?xml version="1.0"?>\n+<!DOCTYPE Blast-db-mask-info PUBLIC "-//NCBI//NCBI BlastDL/EN" "NCBI_BlastDL.dtd">\n+<Blast-db-mask-info>\n+ <Blast-db-mask-info_algo-id>3</Blast-db-mask-info_algo-id>\n+ <Blast-db-mask-info_algo-program>\n+ <Blast-filter-program value="windowmasker">30</Blast-filter-program>\n+ </Blast-db-mask-info_algo-program>\n+ <Blast-db-mask-info_algo-options></Blast-db-mask-info_algo-options>\n+ <Blast-db-mask-info_masks>\n+ <Blast-mask-list>\n+ <Blast-mask-list_masks>\n+ <Seq-loc>\n+ <Seq-loc_packed-int>\n+ <Packed-seqint>\n+ <Seq-interval>\n+ <Seq-interval_from>0</Seq-interval_from>\n+ <Seq-interval_to>13</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>77</Seq-interval_from>\n+ <Seq-interval_to>90</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>208</Seq-interval_from>\n+ <Seq-interval_to>234</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>290</Seq-interval_from>\n+ <Seq-interval_to>314</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>409</Seq-interval_from>\n+ <Seq-interval_to>450</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>479</Seq-interval_from>\n+ <Seq-interval_to>490</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>552</Seq-interval_from>\n+ <Seq-interval_to>566</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>1</Object-id_id>\n+ </Object-id>\n+ '..b'bject-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49062</Seq-interval_from>\n+ <Seq-interval_to>49076</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49156</Seq-interval_from>\n+ <Seq-interval_to>49238</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49433</Seq-interval_from>\n+ <Seq-interval_to>49449</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49496</Seq-interval_from>\n+ <Seq-interval_to>49511</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49701</Seq-interval_from>\n+ <Seq-interval_to>49718</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49887</Seq-interval_from>\n+ <Seq-interval_to>49898</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ <Seq-interval>\n+ <Seq-interval_from>49955</Seq-interval_from>\n+ <Seq-interval_to>49968</Seq-interval_to>\n+ <Seq-interval_id>\n+ <Seq-id>\n+ <Seq-id_local>\n+ <Object-id>\n+ <Object-id_id>2</Object-id_id>\n+ </Object-id>\n+ </Seq-id_local>\n+ </Seq-id>\n+ </Seq-interval_id>\n+ </Seq-interval>\n+ </Packed-seqint>\n+ </Seq-loc_packed-int>\n+ </Seq-loc>\n+ </Blast-mask-list_masks>\n+ <Blast-mask-list_more value="false"/>\n+ </Blast-mask-list>\n+ </Blast-db-mask-info_masks>\n+</Blast-db-mask-info>\n'

diff -r 000000000000 -r f80c9e6700ba tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue May 16 13:18:12 2017 -0400

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="blast" version="2.5.0">
+        <repository changeset_revision="5dd2b68c7d04" name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>

diff -r 000000000000 -r f80c9e6700ba windowmasker_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/windowmasker_macros.xml Tue May 16 13:18:12 2017 -0400

[

@@ -0,0 +1,55 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+        
+            <requirement type="package" version="2.5.0">blast</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @article{Morgulis_2005,
+                    title={WindowMasker: window-based masker for sequenced genomes},
+                    volume={22},
+                    ISSN={1460-2059},
+                    url={http://dx.doi.org/10.1093/bioinformatics/bti774},
+                    DOI={10.1093/bioinformatics/bti774},
+                    number={2}, journal={Bioinformatics},
+                    publisher={Oxford University Press (OUP)},
+                    author={Morgulis, A. and Gertz, E. M. and Schäffer, A. A. and Agarwala, R.},
+                    year={2005}, month={Nov}, pages={134–141}
+                }
+            </citation>
+            <citation type="bibtex">
+                 @article{Cock_2015,
+                    title={NCBI BLAST+ integrated into Galaxy},
+                    volume={4},
+                    ISSN={2047-217X},
+                    url={http://dx.doi.org/10.1186/s13742-015-0080-7},
+                    DOI={10.1186/s13742-015-0080-7},
+                    number={1},
+                    journal={GigaScience},
+                    publisher={Oxford University Press (OUP)},
+                    author={Cock, Peter J. A. and Chilton, John M. and Grüning, Björn and Johnson, James E. and Soranzo, Nicola},
+                    year={2015}, month={Aug}
+                }
+            </citation>
+            <yield />
+        </citations>
+    </xml>
+
+    
+    <token name="@OPTIONAL_PARAM_FUNC@">
+<![CDATA[
+        #def optional_param($_flag, $_flag_value, $_sep=" ")
+            #if str($_flag_value) and str($_flag_value).strip():
+                ${_flag}${_sep}${_flag_value}
+            #end if
+        #end def
+]]>
+    </token>
+</macros>

diff -r 000000000000 -r f80c9e6700ba windowmasker_mkcounts.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/windowmasker_mkcounts.xml Tue May 16 13:18:12 2017 -0400

[

@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<tool id="windowmasker_mkcounts" name="WindowMasker_mkcounts" version="1.0">
+    <description>Construct WindowMasker unit counts table</description>
+
+    <macros>
+        <import>windowmasker_macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <command detect_errors="exit_code">
+<![CDATA[
+    @OPTIONAL_PARAM_FUNC@
+
+    windowmasker -mk_counts -infmt fasta
+
+        $optional_param("-genome_size", $adv.genome_size)
+        $optional_param("-t_low",       $adv.t_low)
+        $optional_param("-t_high",      $adv.t_high)
+        $optional_param("-unit",        $adv.unit)
+
+        -sformat ${adv.sformat} -checkdup ${adv.checkdup}
+        -in "${fasta_input}" -out "${mkcount_output}"
+]]>
+    </command>
+    <inputs>
+        <param name="fasta_input" type="data" format="fasta"
+                label="FASTA sequence file" />
+
+        <section name="adv" title="Advanced options" expanded="false" >
+            <param name="checkdup" type="boolean" checked="false"
+                    truevalue="true" falsevalue="false"
+                    label="Check input file for potentially duplicated sequences"
+                    help="-checkdup" />
+
+            <param name="genome_size" type="integer" label="Genome size"
+                    min="0" optional="true"
+                    help="Use this genome size to compute the unit length" />
+
+            <param name="sformat" type="select" label="Unit counts format"
+                help="The format the unit counts data should be generated" >
+
+                <option value="ascii">Plain text (ascii)</option>
+                <option value="oascii" selected="true">Optimized text (oascii)</option>
+                
+            </param>
+
+            <param name="t_low" type="integer" label="T_low"
+                    min="0" optional="true"
+                    help="Save only units that appears at least this many times" />
+
+            <param name="t_high" type="integer" label="T_high"
+                    min="0" optional="true"
+                    help="Set the maximum count value for units" />
+
+            <param name="unit" type="integer" label="Unit length"
+                    min="1" max="16" optional="true"
+                    help="Unit length used to mask the genome" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="mkcount_output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            
+            <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
+            <output name="mkcount_output" file="chr4_part.oascii.counts" />
+        </test>
+        <test>
+            
+            <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
+            <param name="genome_size" value="500000" />
+            <output name="mkcount_output" file="chr4_part.500k_size.counts" />
+        </test>
+        <test>
+            
+            <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
+            <param name="sformat" value="ascii" />
+            <output name="mkcount_output" file="chr4_part.ascii.counts" />
+        </test>
+        <test>
+            
+            <param name="fasta_input" value="chr4_part.fa" ftype="fasta" />
+            <param name="t_low" value="3" />
+            <param name="t_high" value="20" />
+            <param name="unit" value="9" />
+            <output name="mkcount_output" file="chr4_part.custom_unit.counts" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+This tool runs `stage 1 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_
+of the WindowMasker analysis to produce a unit counts file for a genome assembly.
+
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>

diff -r 000000000000 -r f80c9e6700ba windowmasker_to_bed.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/windowmasker_to_bed.pl Tue May 16 13:18:12 2017 -0400

@@ -0,0 +1,82 @@
+#!/usr/bin/env perl
+use warnings;
+use strict;
+
+=head1 NAME
+
+windowmasker_to_bed.pl - Convert WindowMasker output to BED format
+
+=head1 SYNOPSIS
+
+  windowmasker_to_bed.pl < ${input.interval} > ${output.bed}
+
+=head1 DESCRIPTION
+
+This scripts converts the interval output from WindowMasker ustat
+to bed 4 format.
+
+=head1 VERSION
+
+Last update: 2017-04-28
+
+=cut
+
+
+#====================
+# Libraries
+#====================
+use Getopt::Long;
+use Pod::Usage;
+use Carp;
+
+sub main {
+  parse_arguments();
+
+  my $chrom;
+  my $idx = 0;
+
+  while ( defined(my $line = <>) ) {
+    next if ($line =~ /^\s*$/x);
+
+    if ($line =~ /^>(\S+)/x) {
+      $chrom = $1;
+
+    } elsif ($line =~ /(\d+)\s+\-\s+(\d+)/x) {
+      # interval coordinates are 0-based
+      my $start = $1;
+      my $end = $2 + 1;
+      my $name = sprintf("wm_%d", $idx++);
+
+      print join("\t", $chrom, $start, $end, $name), "\n";
+
+    } else {
+      croak("Invalid line: ${line}");
+    }
+  }
+
+  return;
+}
+
+main();
+
+
+
+#====================
+# Parse command-line arguments
+#====================
+sub parse_arguments {
+  my $help = 0;
+
+  GetOptions('help|?' => \$help) or usage();
+
+  pod2usage({ verbose => 2 }) if ($help);
+
+  return;
+}
+
+sub usage {
+  my $msg = shift;
+
+  pod2usage({ verbose => 1, message => $msg || "" });
+  exit 1;
+}

diff -r 000000000000 -r f80c9e6700ba windowmasker_ustat.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/windowmasker_ustat.xml Tue May 16 13:18:12 2017 -0400

[

b'@@ -0,0 +1,203 @@\n+<?xml version="1.0"?>\n+<tool id="windowmasker_ustat" name="WindowMasker_ustat" version="1.0">\n+ <description>Mask sequences using a WindowMasker unit counts table</description>\n+\n+ <macros>\n+ <import>windowmasker_macros.xml</import>\n+ </macros>\n+\n+ <expand macro="requirements" />\n+\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+ @OPTIONAL_PARAM_FUNC@\n+\n+ windowmasker -ustat "${mkcount_input}"\n+ -infmt fasta\n+ -in "${fasta_input}"\n+ -outfmt "${output_format}"\n+ ${parse_seqids}\n+\n+ #if str($use_dust.use_dust_selector) == "yes":\n+ -dust true -dust_level ${use_dust.dust_level}\n+ #end if\n+\n+ $optional_param("-set_t_high", $adv.set_t_high)\n+ $optional_param("-set_t_low", $adv.set_t_low)\n+ $optional_param("-t_extend", $adv.t_extend)\n+ $optional_param("-t_low", $adv.t_low)\n+ $optional_param("-t_high", $adv.t_high)\n+ $optional_param("-t_thres", $adv.t_thres)\n+ $optional_param("-window", $adv.window)\n+\n+ ## Convert WindowMasker interval output to BED format\n+ #if str($output_format) == "interval":\n+ | ${__tool_directory__}/windowmasker_to_bed.pl > "${mask_output}"\n+ #else\n+ -out "${mask_output}"\n+ #end if\n+]]>\n+ </command>\n+ <inputs>\n+ <param name="fasta_input" type="data" format="fasta"\n+ label="FASTA sequence file" />\n+\n+ <param name="mkcount_input" type="data" format="txt"\n+ label="Unit counts produced by WindowMasker mkcount" />\n+\n+ <param name="parse_seqids" type="boolean" checked="false"\n+ truevalue="-parse_seqids" falsevalue=""\n+ label="Parse Seq-ids in FASTA input"\n+ help="-parse_seqids" />\n+\n+ <conditional name="use_dust">\n+ <param name="use_dust_selector" type="select"\n+ label="Use DUST to mask low complexity sequences?"\n+ help="-dust">\n+ <option value="yes">Yes</option>\n+ <option value="no">No</option>\n+ </param>\n+\n+ <when value="yes">\n+ <param name="dust_level" type="integer"\n+ min="1" value="20"\n+ label="DUST level"\n+ help="Score threshold for subwindows" />\n+ </when>\n+\n+ <when value="no"></when>\n+ </conditional>\n+\n+ <param name="output_format" type="select" label="Output format">\n+ <option value="fasta">FASTA</option>\n+ <option value="interval" selected="true">BED</option>\n+ <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option>\n+ <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option>\n+ <option value="maskinfo_xml">maskinfo XML</option>\n+ </param>\n+\n+ <section name="adv" title="Advanced options" expanded="false">\n+\n+ <param name="set_t_high" type="integer" label="set_t_high"\n+ min="0" optional="true"\n+ help="Score for units with unit count greater than T_high" />\n+\n+ <param name="set_t_low" type="integer" label="set_t_low"\n+ min="0" optional="true"\n+ help="Score for units with unit count less than T_low" />\n+\n+ <param name="t_extend" type="integer" label="t_extend"\n+ min="0" optional="true"\n+ help="Override the t_extend value in the unit counts file" />\n+\n+ <param name="t_low" type="integer" label="t_low"\n+ min="0" optional="true"\n+ help="Override the t_low value in the unit counts file" />\n+\n+ <param name="t_high" type="integer" label="t_high"\n+ min="0" optional="true"\n+ help="Override the t_high value in the unit counts file" />\n+\n+ <param name="t_t'..b' </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="output_format" value="fasta" />\n+ <output name="mask_output" file="contigs.wm.fa" />\n+ </test>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="output_format" value="maskinfo_asn1_text" />\n+ <output name="mask_output" file="contigs.wm.asn1" />\n+ </test>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="output_format" value="maskinfo_asn1_bin" />\n+ <output name="mask_output" file="contigs.wm.asnb" />\n+ </test>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="output_format" value="maskinfo_xml" />\n+ <output name="mask_output" file="contigs.wm.xml" />\n+ </test>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="set_t_high" value="10" />\n+ <param name="set_t_low" value="9" />\n+ <param name="t_extend" value="5" />\n+ <param name="t_low" value="9" />\n+ <param name="t_high" value="10" />\n+ <param name="t_thres" value="20" />\n+ <param name="window" value="50" />\n+ <output name="mask_output" file="contigs.advanced_wm.bed" />\n+ </test>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="use_dust_selector" value="no" />\n+ <output name="mask_output" file="contigs.nodust_wm.bed" />\n+ </test>\n+ <test>\n+ \n+ <param name="fasta_input" value="contigs.fa" ftype="fasta" />\n+ <param name="mkcount_input" value="chr4_part.oascii.counts" ftype="txt" />\n+ <param name="parse_seqids" value="-parse_seqids" />\n+ <output name="mask_output" file="contigs.seqid_wm.bed" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+**What it does**\n+\n+This tool runs `stage 2 <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/>`_\n+of the WindowMasker analysis to identify repeats within the input sequences.\n+\n+.. class:: infomark\n+\n+**Output formats:**\n+\n+* Use the **binary or text maskinfo ASN.1** output formats to generate the mask file for\n+ the `NCBI BLAST+ makeblastdb tool <https://www.ncbi.nlm.nih.gov/books/NBK279681/#_cookbook_Create_BLAST_database_with_the_>`_\n+* Use the BED output format to generate a list of masked regions\n+\n+\n+.. class:: infomark\n+\n+**Advanced options:**\n+\n+* See the `WindowMasker README file <https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/README>`_\n+ for additional details on the WindowMasker repeat masking options\n+\n+ ]]></help>\n+\n+ <expand macro="citations" />\n+</tool>\n'