Mercurial > repos > artbio > small_rna_maps

changeset 30:183bf49fe77c draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
author artbio
date Sat, 05 Oct 2019 18:25:19 -0400
parents 8b5695592784
children f82badb66c34
files small_rna_maps.py small_rna_maps.r small_rna_maps.xml test-data/clustering.pdf test-data/clustering_unstranded.pdf test-data/global_merge.pdf test-data/global_nomerge.pdf test-data/input1__single_plot_mean.pdf test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf test-data/input1_input2_norm_1_2_single_plot_counts.pdf test-data/input1_input2new_norm_1_2_single_plot_counts.pdf test-data/input1_min20_max30_single_plot_size.pdf test-data/input1_single_plot_median.pdf test-data/input1_yminneg5_5_single_plot_counts.pdf test-data/input_single_chr_x_6_single_plot_coverage.pdf test-data/size.tab test-data/size1.bam test-data/size12.tab test-data/size2.bam
diffstat 19 files changed, 1650 insertions(+), 702 deletions(-) [+]
line wrap: on
line diff
--- a/small_rna_maps.py	Fri Oct 04 04:33:53 2019 -0400
+++ b/small_rna_maps.py	Sat Oct 05 18:25:19 2019 -0400
@@ -242,6 +242,8 @@
                     if not map_dictionary[(chrom, pos+1, 'F')]:
                         map_dictionary[(chrom, pos+1, 'F')] = []
         for key in map_dictionary:
+            if 'R' in key:
+                continue
             coverage = self.bam_object.count_coverage(
                                                 contig=key[0],
                                                 start=key[1]-1,
--- a/small_rna_maps.r	Fri Oct 04 04:33:53 2019 -0400
+++ b/small_rna_maps.r	Sat Oct 05 18:25:19 2019 -0400
@@ -26,9 +26,12 @@
 args = parse_args(parser)
 
 # data frames implementation
+
 ## first table
 Table = read.delim(args$first_dataframe, header=T, row.names=NULL)
 colnames(Table)[1] <- "Dataset"
+dropcol <- c("Strandness", "z.score") # not used by this Rscript and is dropped for backward compatibility
+Table <- Table[,!(names(Table) %in% dropcol)]
 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
   Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
 }
@@ -42,6 +45,9 @@
 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size" | args$first_plot_method == "Coverage") {
   i = 1
   for (sample in samples) {
+    # Warning
+    # Here the column is hard coded as the last column (dangerous)
+    # because its name changes with the method
     Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i]
     i = i + 1
   }
@@ -50,10 +56,13 @@
 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
 n_genes=length(per_gene_readmap)
+
 # second table
 if (args$extra_plot_method != '') {
   ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
   colnames(ExtraTable)[1] <- "Dataset"
+  dropcol <- c("Strandness", "z.score") # not used by this Rscript and is dropped for backward compatibility
+  Table <- Table[,!(names(Table) %in% dropcol)]
   if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') {
     ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
   }
@@ -134,10 +143,10 @@
   } else if (method != "Size") {
     p = xyplot(eval(as.name(method))~Coordinate|factor(Dataset, levels=unique(Dataset))+factor(Chromosome, levels=unique(Chromosome)),
                data=df,
-               type='p',
+               type= ifelse(method=='Coverage', 'l', 'p'),
                pch=19,
                cex=0.35,
-               scales= list(relation="free", x=list(rot=0, cex=0.7, tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+               scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
                xlab=NULL, main=NULL, ylab=NULL, ylim=ylimits,
                as.table=T,
                origin = 0,
@@ -146,6 +155,7 @@
                col=c("red","blue"),
                par.strip.text = list(cex=0.7),
                ...)
+    p=combineLimits(p)
   } else {
     p = barchart(Counts~as.factor(Size)|factor(Dataset, levels=unique(Dataset))+Chromosome, data = df, origin = 0,
                  horizontal=FALSE,
--- a/small_rna_maps.xml	Fri Oct 04 04:33:53 2019 -0400
+++ b/small_rna_maps.xml	Sat Oct 05 18:25:19 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.15.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.16.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -302,21 +302,21 @@
             <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
         </test>
         <test> <!-- 13 -->
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
-            <param name="normalization" value="1.0 1.0" />
+            <param name="inputs" value="size1.bam,size2.bam" ftype="bam" />
+            <param name="normalization" value="2.0 1.0" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="nomerge" />
             <param name="first_plot" value="Size" />
-            <output file="size.tab" name="output_tab" />
+            <output file="size12.tab" name="output_tab" />
             <output file="global_nomerge.pdf" name="output_pdf" />
         </test>
         <test> <!-- 14 -->
-            <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
-            <param name="normalization" value="1.0 1.0" />
+            <param name="inputs" value="size1.bam,size2.bam" ftype="bam" />
+            <param name="normalization" value="2.0 1.0" />
             <param name="plots_options_selector" value="global" />
             <param name="mergestrands" value="merge" />
             <param name="first_plot" value="Size" />
-            <output file="size.tab" name="output_tab" />
+            <output file="size12.tab" name="output_tab" />
             <output file="global_merge.pdf" name="output_pdf" />
         </test>
     </tests>
Binary file test-data/clustering.pdf has changed
Binary file test-data/clustering_unstranded.pdf has changed
Binary file test-data/global_merge.pdf has changed
Binary file test-data/global_nomerge.pdf has changed
Binary file test-data/input1__single_plot_mean.pdf has changed
Binary file test-data/input1_input2_double_plot_counts_size_ylimneg5_5.pdf has changed
Binary file test-data/input1_input2_norm_1_2_single_plot_counts.pdf has changed
Binary file test-data/input1_input2new_norm_1_2_single_plot_counts.pdf has changed
Binary file test-data/input1_min20_max30_single_plot_size.pdf has changed
Binary file test-data/input1_single_plot_median.pdf has changed
Binary file test-data/input1_yminneg5_5_single_plot_counts.pdf has changed
Binary file test-data/input_single_chr_x_6_single_plot_coverage.pdf has changed
--- a/test-data/size.tab	Fri Oct 04 04:33:53 2019 -0400
+++ b/test-data/size.tab	Sat Oct 05 18:25:19 2019 -0400
@@ -1,694 +1,815 @@
 # Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
-input1.bam	FBtr0070001	F	19	1	1.0	-0.449
-input1.bam	FBtr0070001	F	20	4	1.0	-0.104
-input1.bam	FBtr0070001	F	21	4	1.0	-0.104
-input1.bam	FBtr0070001	F	22	29	1.0	2.765
-input1.bam	FBtr0070001	F	23	15	1.0	1.158
-input1.bam	FBtr0070001	F	24	1	1.0	-0.449
-input1.bam	FBtr0070001	F	25	0	1.0	-0.563
-input1.bam	FBtr0070001	F	26	0	1.0	-0.563
-input1.bam	FBtr0070001	F	27	0	1.0	-0.563
-input1.bam	FBtr0070001	F	28	0	1.0	-0.563
-input1.bam	FBtr0070001	F	29	0	1.0	-0.563
-input1.bam	FBtr0070533	F	19	3	1.0	1.275
-input1.bam	FBtr0070533	F	20	2	1.0	0.537
-input1.bam	FBtr0070533	F	21	2	1.0	0.537
-input1.bam	FBtr0070533	F	22	4	1.0	2.013
-input1.bam	FBtr0070533	F	23	2	1.0	0.537
-input1.bam	FBtr0070533	F	24	0	1.0	-0.94
-input1.bam	FBtr0070533	F	25	1	1.0	-0.201
-input1.bam	FBtr0070533	F	26	0	1.0	-0.94
-input1.bam	FBtr0070533	F	27	0	1.0	-0.94
-input1.bam	FBtr0070533	F	28	0	1.0	-0.94
-input1.bam	FBtr0070533	F	29	0	1.0	-0.94
-input1.bam	FBtr0070603	F	19	1	1.0	-0.874
-input1.bam	FBtr0070603	F	20	6	1.0	0.907
-input1.bam	FBtr0070603	F	21	3	1.0	-0.162
-input1.bam	FBtr0070603	F	22	3	1.0	-0.162
-input1.bam	FBtr0070603	F	23	10	1.0	2.331
-input1.bam	FBtr0070603	F	24	2	1.0	-0.518
-input1.bam	FBtr0070603	F	25	5	1.0	0.55
-input1.bam	FBtr0070603	F	26	5	1.0	0.55
-input1.bam	FBtr0070603	F	27	3	1.0	-0.162
-input1.bam	FBtr0070603	F	28	0	1.0	-1.23
-input1.bam	FBtr0070603	F	29	0	1.0	-1.23
-input1.bam	FBtr0070604	F	19	2	1.0	-0.186
-input1.bam	FBtr0070604	F	20	0	1.0	-0.478
-input1.bam	FBtr0070604	F	21	1	1.0	-0.332
-input1.bam	FBtr0070604	F	22	23	1.0	2.88
-input1.bam	FBtr0070604	F	23	10	1.0	0.982
-input1.bam	FBtr0070604	F	24	0	1.0	-0.478
-input1.bam	FBtr0070604	F	25	0	1.0	-0.478
-input1.bam	FBtr0070604	F	26	0	1.0	-0.478
-input1.bam	FBtr0070604	F	27	0	1.0	-0.478
-input1.bam	FBtr0070604	F	28	0	1.0	-0.478
-input1.bam	FBtr0070604	F	29	0	1.0	-0.478
-input1.bam	FBtr0070911	F	19	0	1.0	-0.316
-input1.bam	FBtr0070911	F	20	0	1.0	-0.316
-input1.bam	FBtr0070911	F	21	1	1.0	3.162
-input1.bam	FBtr0070911	F	22	0	1.0	-0.316
-input1.bam	FBtr0070911	F	23	0	1.0	-0.316
-input1.bam	FBtr0070911	F	24	0	1.0	-0.316
-input1.bam	FBtr0070911	F	25	0	1.0	-0.316
-input1.bam	FBtr0070911	F	26	0	1.0	-0.316
-input1.bam	FBtr0070911	F	27	0	1.0	-0.316
-input1.bam	FBtr0070911	F	28	0	1.0	-0.316
-input1.bam	FBtr0070911	F	29	0	1.0	-0.316
-input1.bam	FBtr0078490	F	19	0	1.0	-0.316
-input1.bam	FBtr0078490	F	20	0	1.0	-0.316
-input1.bam	FBtr0078490	F	21	0	1.0	-0.316
-input1.bam	FBtr0078490	F	22	0	1.0	-0.316
-input1.bam	FBtr0078490	F	23	1	1.0	3.162
-input1.bam	FBtr0078490	F	24	0	1.0	-0.316
-input1.bam	FBtr0078490	F	25	0	1.0	-0.316
-input1.bam	FBtr0078490	F	26	0	1.0	-0.316
-input1.bam	FBtr0078490	F	27	0	1.0	-0.316
-input1.bam	FBtr0078490	F	28	0	1.0	-0.316
-input1.bam	FBtr0078490	F	29	0	1.0	-0.316
-input1.bam	FBtr0078580	F	19	8	1.0	-0.45
-input1.bam	FBtr0078580	F	20	9	1.0	-0.437
-input1.bam	FBtr0078580	F	21	5	1.0	-0.491
-input1.bam	FBtr0078580	F	22	13	1.0	-0.382
-input1.bam	FBtr0078580	F	23	5	1.0	-0.491
-input1.bam	FBtr0078580	F	24	180	1.0	1.89
-input1.bam	FBtr0078580	F	25	212	1.0	2.325
-input1.bam	FBtr0078580	F	26	1	1.0	-0.545
-input1.bam	FBtr0078580	F	27	2	1.0	-0.532
-input1.bam	FBtr0078580	F	28	17	1.0	-0.328
-input1.bam	FBtr0078580	F	29	0	1.0	-0.559
-input1.bam	FBtr0078790	F	19	2	1.0	1.547
-input1.bam	FBtr0078790	F	20	2	1.0	1.547
-input1.bam	FBtr0078790	F	21	0	1.0	-0.722
-input1.bam	FBtr0078790	F	22	2	1.0	1.547
-input1.bam	FBtr0078790	F	23	1	1.0	0.413
-input1.bam	FBtr0078790	F	24	0	1.0	-0.722
-input1.bam	FBtr0078790	F	25	0	1.0	-0.722
-input1.bam	FBtr0078790	F	26	0	1.0	-0.722
-input1.bam	FBtr0078790	F	27	0	1.0	-0.722
-input1.bam	FBtr0078790	F	28	0	1.0	-0.722
-input1.bam	FBtr0078790	F	29	0	1.0	-0.722
-input1.bam	FBtr0079064	F	19	0	1.0	-0.316
-input1.bam	FBtr0079064	F	20	0	1.0	-0.316
-input1.bam	FBtr0079064	F	21	1	1.0	3.162
-input1.bam	FBtr0079064	F	22	0	1.0	-0.316
-input1.bam	FBtr0079064	F	23	0	1.0	-0.316
-input1.bam	FBtr0079064	F	24	0	1.0	-0.316
-input1.bam	FBtr0079064	F	25	0	1.0	-0.316
-input1.bam	FBtr0079064	F	26	0	1.0	-0.316
-input1.bam	FBtr0079064	F	27	0	1.0	-0.316
-input1.bam	FBtr0079064	F	28	0	1.0	-0.316
-input1.bam	FBtr0079064	F	29	0	1.0	-0.316
-input1.bam	FBtr0079090	F	19	0	0.67	-0.612
-input1.bam	FBtr0079090	F	20	0	0.67	-0.612
-input1.bam	FBtr0079090	F	21	0	0.67	1.633
-input1.bam	FBtr0079090	F	22	0	0.67	-0.612
-input1.bam	FBtr0079090	F	23	0	0.67	-0.612
-input1.bam	FBtr0079090	F	24	1	0.67	1.633
-input1.bam	FBtr0079090	F	25	0	0.67	-0.612
-input1.bam	FBtr0079090	F	26	0	0.67	-0.612
-input1.bam	FBtr0079090	F	27	0	0.67	-0.612
-input1.bam	FBtr0079090	F	28	1	0.67	1.633
-input1.bam	FBtr0079090	F	29	0	0.67	-0.612
-input1.bam	FBtr0079090	R	19	0	0.67	-0.612
-input1.bam	FBtr0079090	R	20	0	0.67	-0.612
-input1.bam	FBtr0079090	R	21	1	0.67	1.633
-input1.bam	FBtr0079090	R	22	0	0.67	-0.612
-input1.bam	FBtr0079090	R	23	0	0.67	-0.612
-input1.bam	FBtr0079090	R	24	0	0.67	1.633
-input1.bam	FBtr0079090	R	25	0	0.67	-0.612
-input1.bam	FBtr0079090	R	26	0	0.67	-0.612
-input1.bam	FBtr0079090	R	27	0	0.67	-0.612
-input1.bam	FBtr0079090	R	28	0	0.67	1.633
-input1.bam	FBtr0079090	R	29	0	0.67	-0.612
-input1.bam	FBtr0079338	F	19	1	1.0	0.05
-input1.bam	FBtr0079338	F	20	0	1.0	-0.496
-input1.bam	FBtr0079338	F	21	3	1.0	1.141
-input1.bam	FBtr0079338	F	22	6	1.0	2.779
-input1.bam	FBtr0079338	F	23	0	1.0	-0.496
-input1.bam	FBtr0079338	F	24	0	1.0	-0.496
-input1.bam	FBtr0079338	F	25	0	1.0	-0.496
-input1.bam	FBtr0079338	F	26	0	1.0	-0.496
-input1.bam	FBtr0079338	F	27	0	1.0	-0.496
-input1.bam	FBtr0079338	F	28	0	1.0	-0.496
-input1.bam	FBtr0079338	F	29	0	1.0	-0.496
-input1.bam	FBtr0079528	F	19	4	1.0	-0.321
-input1.bam	FBtr0079528	F	20	12	1.0	0.509
-input1.bam	FBtr0079528	F	21	3	1.0	-0.424
-input1.bam	FBtr0079528	F	22	2	1.0	-0.528
-input1.bam	FBtr0079528	F	23	3	1.0	-0.424
-input1.bam	FBtr0079528	F	24	36	1.0	2.998
-input1.bam	FBtr0079528	F	25	8	1.0	0.094
-input1.bam	FBtr0079528	F	26	5	1.0	-0.217
-input1.bam	FBtr0079528	F	27	2	1.0	-0.528
-input1.bam	FBtr0079528	F	28	2	1.0	-0.528
-input1.bam	FBtr0079528	F	29	1	1.0	-0.632
-input1.bam	FBtr0079596	F	19	10	1.0	0.912
-input1.bam	FBtr0079596	F	20	13	1.0	1.449
-input1.bam	FBtr0079596	F	21	3	1.0	-0.342
-input1.bam	FBtr0079596	F	22	16	1.0	1.986
-input1.bam	FBtr0079596	F	23	8	1.0	0.554
-input1.bam	FBtr0079596	F	24	0	1.0	-0.879
-input1.bam	FBtr0079596	F	25	0	1.0	-0.879
-input1.bam	FBtr0079596	F	26	3	1.0	-0.342
-input1.bam	FBtr0079596	F	27	1	1.0	-0.7
-input1.bam	FBtr0079596	F	28	0	1.0	-0.879
-input1.bam	FBtr0079596	F	29	0	1.0	-0.879
-input1.bam	FBtr0079677	F	19	2	1.0	2.801
-input1.bam	FBtr0079677	F	20	0	1.0	-0.442
-input1.bam	FBtr0079677	F	21	0	1.0	-0.442
-input1.bam	FBtr0079677	F	22	0	1.0	-0.442
-input1.bam	FBtr0079677	F	23	1	1.0	1.18
-input1.bam	FBtr0079677	F	24	0	1.0	-0.442
-input1.bam	FBtr0079677	F	25	0	1.0	-0.442
-input1.bam	FBtr0079677	F	26	0	1.0	-0.442
-input1.bam	FBtr0079677	F	27	0	1.0	-0.442
-input1.bam	FBtr0079677	F	28	0	1.0	-0.442
-input1.bam	FBtr0079677	F	29	0	1.0	-0.442
-input1.bam	FBtr0079690	F	19	0	1.0	-0.316
-input1.bam	FBtr0079690	F	20	0	1.0	-0.316
-input1.bam	FBtr0079690	F	21	0	1.0	-0.316
-input1.bam	FBtr0079690	F	22	0	1.0	-0.316
-input1.bam	FBtr0079690	F	23	0	1.0	-0.316
-input1.bam	FBtr0079690	F	24	0	1.0	-0.316
-input1.bam	FBtr0079690	F	25	1	1.0	3.162
-input1.bam	FBtr0079690	F	26	0	1.0	-0.316
-input1.bam	FBtr0079690	F	27	0	1.0	-0.316
-input1.bam	FBtr0079690	F	28	0	1.0	-0.316
-input1.bam	FBtr0079690	F	29	0	1.0	-0.316
-input1.bam	FBtr0079692	F	19	1	1.0	1.633
-input1.bam	FBtr0079692	F	20	1	1.0	1.633
-input1.bam	FBtr0079692	F	21	0	1.0	-0.612
-input1.bam	FBtr0079692	F	22	0	1.0	-0.612
-input1.bam	FBtr0079692	F	23	1	1.0	1.633
-input1.bam	FBtr0079692	F	24	0	1.0	-0.612
-input1.bam	FBtr0079692	F	25	0	1.0	-0.612
-input1.bam	FBtr0079692	F	26	0	1.0	-0.612
-input1.bam	FBtr0079692	F	27	0	1.0	-0.612
-input1.bam	FBtr0079692	F	28	0	1.0	-0.612
-input1.bam	FBtr0079692	F	29	0	1.0	-0.612
-input1.bam	FBtr0079693	F	19	0	1.0	-0.471
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+size2.bam	PbANKA_05_v3	F	28	4	0.11	-0.027
+size2.bam	PbANKA_05_v3	F	29	11	0.11	-1.641
+size2.bam	PbANKA_05_v3	R	19	75	0.11	-1.201
+size2.bam	PbANKA_05_v3	R	20	117	0.11	1.881
+size2.bam	PbANKA_05_v3	R	21	109	0.11	0.927
+size2.bam	PbANKA_05_v3	R	22	104	0.11	1.074
+size2.bam	PbANKA_05_v3	R	23	99	0.11	0.267
+size2.bam	PbANKA_05_v3	R	24	94	0.11	0.414
+size2.bam	PbANKA_05_v3	R	25	89	0.11	-0.394
+size2.bam	PbANKA_05_v3	R	26	83	0.11	-0.834
+size2.bam	PbANKA_05_v3	R	27	90	0.11	-0.467
+size2.bam	PbANKA_05_v3	R	28	101	0.11	-0.027
+size2.bam	PbANKA_05_v3	R	29	72	0.11	-1.641
+size2.bam	PbANKA_06_v3	F	19	12	0.12	-0.709
+size2.bam	PbANKA_06_v3	F	20	18	0.12	0.732
+size2.bam	PbANKA_06_v3	F	21	14	0.12	0.224
+size2.bam	PbANKA_06_v3	F	22	15	0.12	1.326
+size2.bam	PbANKA_06_v3	F	23	9	0.12	0.647
+size2.bam	PbANKA_06_v3	F	24	16	0.12	0.139
+size2.bam	PbANKA_06_v3	F	25	9	0.12	1.41
+size2.bam	PbANKA_06_v3	F	26	12	0.12	0.224
+size2.bam	PbANKA_06_v3	F	27	13	0.12	-1.387
+size2.bam	PbANKA_06_v3	F	28	10	0.12	-0.879
+size2.bam	PbANKA_06_v3	F	29	11	0.12	-1.726
+size2.bam	PbANKA_06_v3	R	19	88	0.12	-0.709
+size2.bam	PbANKA_06_v3	R	20	99	0.12	0.732
+size2.bam	PbANKA_06_v3	R	21	97	0.12	0.224
+size2.bam	PbANKA_06_v3	R	22	109	0.12	1.326
+size2.bam	PbANKA_06_v3	R	23	107	0.12	0.647
+size2.bam	PbANKA_06_v3	R	24	94	0.12	0.139
+size2.bam	PbANKA_06_v3	R	25	116	0.12	1.41
+size2.bam	PbANKA_06_v3	R	26	99	0.12	0.224
+size2.bam	PbANKA_06_v3	R	27	79	0.12	-1.387
+size2.bam	PbANKA_06_v3	R	28	88	0.12	-0.879
+size2.bam	PbANKA_06_v3	R	29	77	0.12	-1.726
+size2.bam	PbANKA_07_v3	F	19	12	0.04	-1.18
+size2.bam	PbANKA_07_v3	F	20	9	0.04	0.324
+size2.bam	PbANKA_07_v3	F	21	13	0.04	2.025
+size2.bam	PbANKA_07_v3	F	22	8	0.04	1.392
+size2.bam	PbANKA_07_v3	F	23	10	0.04	-0.349
+size2.bam	PbANKA_07_v3	F	24	9	0.04	-0.982
+size2.bam	PbANKA_07_v3	F	25	8	0.04	0.205
+size2.bam	PbANKA_07_v3	F	26	6	0.04	0.403
+size2.bam	PbANKA_07_v3	F	27	10	0.04	-0.863
+size2.bam	PbANKA_07_v3	F	28	7	0.04	0.205
+size2.bam	PbANKA_07_v3	F	29	5	0.04	-1.18
+size2.bam	PbANKA_07_v3	R	19	185	0.04	-1.18
+size2.bam	PbANKA_07_v3	R	20	226	0.04	0.324
+size2.bam	PbANKA_07_v3	R	21	265	0.04	2.025
+size2.bam	PbANKA_07_v3	R	22	254	0.04	1.392
+size2.bam	PbANKA_07_v3	R	23	208	0.04	-0.349
+size2.bam	PbANKA_07_v3	R	24	193	0.04	-0.982
+size2.bam	PbANKA_07_v3	R	25	224	0.04	0.205
+size2.bam	PbANKA_07_v3	R	26	231	0.04	0.403
+size2.bam	PbANKA_07_v3	R	27	195	0.04	-0.863
+size2.bam	PbANKA_07_v3	R	28	225	0.04	0.205
+size2.bam	PbANKA_07_v3	R	29	192	0.04	-1.18
+size2.bam	PbANKA_08_v3	F	19	12	0.44	0.66
+size2.bam	PbANKA_08_v3	F	20	13	0.44	-0.22
+size2.bam	PbANKA_08_v3	F	21	32	0.44	1.871
+size2.bam	PbANKA_08_v3	F	22	21	0.44	1.321
+size2.bam	PbANKA_08_v3	F	23	17	0.44	0.33
+size2.bam	PbANKA_08_v3	F	24	22	0.44	0.55
+size2.bam	PbANKA_08_v3	F	25	11	0.44	-0.66
+size2.bam	PbANKA_08_v3	F	26	9	0.44	-1.321
+size2.bam	PbANKA_08_v3	F	27	13	0.44	-0.66
+size2.bam	PbANKA_08_v3	F	28	7	0.44	-1.431
+size2.bam	PbANKA_08_v3	F	29	12	0.44	-0.44
+size2.bam	PbANKA_08_v3	R	19	29	0.44	0.66
+size2.bam	PbANKA_08_v3	R	20	20	0.44	-0.22
+size2.bam	PbANKA_08_v3	R	21	20	0.44	1.871
+size2.bam	PbANKA_08_v3	R	22	26	0.44	1.321
+size2.bam	PbANKA_08_v3	R	23	21	0.44	0.33
+size2.bam	PbANKA_08_v3	R	24	18	0.44	0.55
+size2.bam	PbANKA_08_v3	R	25	18	0.44	-0.66
+size2.bam	PbANKA_08_v3	R	26	14	0.44	-1.321
+size2.bam	PbANKA_08_v3	R	27	16	0.44	-0.66
+size2.bam	PbANKA_08_v3	R	28	15	0.44	-1.431
+size2.bam	PbANKA_08_v3	R	29	19	0.44	-0.44
+size2.bam	PbANKA_09_v3	F	19	22	0.45	1.726
+size2.bam	PbANKA_09_v3	F	20	17	0.45	-0.368
+size2.bam	PbANKA_09_v3	F	21	23	0.45	1.028
+size2.bam	PbANKA_09_v3	F	22	22	0.45	1.167
+size2.bam	PbANKA_09_v3	F	23	22	0.45	0.888
+size2.bam	PbANKA_09_v3	F	24	15	0.45	-0.926
+size2.bam	PbANKA_09_v3	F	25	11	0.45	-0.368
+size2.bam	PbANKA_09_v3	F	26	16	0.45	-0.368
+size2.bam	PbANKA_09_v3	F	27	12	0.45	-0.228
+size2.bam	PbANKA_09_v3	F	28	12	0.45	-1.624
+size2.bam	PbANKA_09_v3	F	29	11	0.45	-0.926
+size2.bam	PbANKA_09_v3	R	19	27	0.45	1.726
+size2.bam	PbANKA_09_v3	R	20	17	0.45	-0.368
+size2.bam	PbANKA_09_v3	R	21	21	0.45	1.028
+size2.bam	PbANKA_09_v3	R	22	23	0.45	1.167
+size2.bam	PbANKA_09_v3	R	23	21	0.45	0.888
+size2.bam	PbANKA_09_v3	R	24	15	0.45	-0.926
+size2.bam	PbANKA_09_v3	R	25	23	0.45	-0.368
+size2.bam	PbANKA_09_v3	R	26	18	0.45	-0.368
+size2.bam	PbANKA_09_v3	R	27	23	0.45	-0.228
+size2.bam	PbANKA_09_v3	R	28	13	0.45	-1.624
+size2.bam	PbANKA_09_v3	R	29	19	0.45	-0.926
+size2.bam	PbANKA_10_v3	F	19	54	0.58	1.527
+size2.bam	PbANKA_10_v3	F	20	45	0.58	1.036
+size2.bam	PbANKA_10_v3	F	21	39	0.58	0.545
+size2.bam	PbANKA_10_v3	F	22	34	0.58	0.348
+size2.bam	PbANKA_10_v3	F	23	41	0.58	0.937
+size2.bam	PbANKA_10_v3	F	24	35	0.58	0.741
+size2.bam	PbANKA_10_v3	F	25	30	0.58	-1.027
+size2.bam	PbANKA_10_v3	F	26	22	0.58	-1.125
+size2.bam	PbANKA_10_v3	F	27	26	0.58	-0.437
+size2.bam	PbANKA_10_v3	F	28	23	0.58	-1.321
+size2.bam	PbANKA_10_v3	F	29	23	0.58	-1.223
+size2.bam	PbANKA_10_v3	R	19	20	0.58	1.527
+size2.bam	PbANKA_10_v3	R	20	24	0.58	1.036
+size2.bam	PbANKA_10_v3	R	21	25	0.58	0.545
+size2.bam	PbANKA_10_v3	R	22	28	0.58	0.348
+size2.bam	PbANKA_10_v3	R	23	27	0.58	0.937
+size2.bam	PbANKA_10_v3	R	24	31	0.58	0.741
+size2.bam	PbANKA_10_v3	R	25	18	0.58	-1.027
+size2.bam	PbANKA_10_v3	R	26	25	0.58	-1.125
+size2.bam	PbANKA_10_v3	R	27	28	0.58	-0.437
+size2.bam	PbANKA_10_v3	R	28	22	0.58	-1.321
+size2.bam	PbANKA_10_v3	R	29	23	0.58	-1.223
+size2.bam	PbANKA_11_v3	F	19	28	0.44	0.585
+size2.bam	PbANKA_11_v3	F	20	22	0.44	0.08
+size2.bam	PbANKA_11_v3	F	21	25	0.44	1.216
+size2.bam	PbANKA_11_v3	F	22	20	0.44	1.216
+size2.bam	PbANKA_11_v3	F	23	18	0.44	-0.677
+size2.bam	PbANKA_11_v3	F	24	21	0.44	-1.056
+size2.bam	PbANKA_11_v3	F	25	19	0.44	0.711
+size2.bam	PbANKA_11_v3	F	26	17	0.44	-0.551
+size2.bam	PbANKA_11_v3	F	27	25	0.44	1.216
+size2.bam	PbANKA_11_v3	F	28	13	0.44	-1.182
+size2.bam	PbANKA_11_v3	F	29	14	0.44	-1.56
+size2.bam	PbANKA_11_v3	R	19	22	0.44	0.585
+size2.bam	PbANKA_11_v3	R	20	24	0.44	0.08
+size2.bam	PbANKA_11_v3	R	21	30	0.44	1.216
+size2.bam	PbANKA_11_v3	R	22	35	0.44	1.216
+size2.bam	PbANKA_11_v3	R	23	22	0.44	-0.677
+size2.bam	PbANKA_11_v3	R	24	16	0.44	-1.056
+size2.bam	PbANKA_11_v3	R	25	32	0.44	0.711
+size2.bam	PbANKA_11_v3	R	26	24	0.44	-0.551
+size2.bam	PbANKA_11_v3	R	27	30	0.44	1.216
+size2.bam	PbANKA_11_v3	R	28	23	0.44	-1.182
+size2.bam	PbANKA_11_v3	R	29	19	0.44	-1.56
+size2.bam	PbANKA_12_v3	F	19	22	0.07	-1.157
+size2.bam	PbANKA_12_v3	F	20	23	0.07	1.377
+size2.bam	PbANKA_12_v3	F	21	27	0.07	1.008
+size2.bam	PbANKA_12_v3	F	22	13	0.07	1.8
+size2.bam	PbANKA_12_v3	F	23	13	0.07	-1.104
+size2.bam	PbANKA_12_v3	F	24	17	0.07	0.163
+size2.bam	PbANKA_12_v3	F	25	13	0.07	0.058
+size2.bam	PbANKA_12_v3	F	26	25	0.07	0.374
+size2.bam	PbANKA_12_v3	F	27	17	0.07	-0.893
+size2.bam	PbANKA_12_v3	F	28	26	0.07	-0.84
+size2.bam	PbANKA_12_v3	F	29	14	0.07	-0.787
+size2.bam	PbANKA_12_v3	R	19	223	0.07	-1.157
+size2.bam	PbANKA_12_v3	R	20	270	0.07	1.377
+size2.bam	PbANKA_12_v3	R	21	259	0.07	1.008
+size2.bam	PbANKA_12_v3	R	22	288	0.07	1.8
+size2.bam	PbANKA_12_v3	R	23	233	0.07	-1.104
+size2.bam	PbANKA_12_v3	R	24	253	0.07	0.163
+size2.bam	PbANKA_12_v3	R	25	255	0.07	0.058
+size2.bam	PbANKA_12_v3	R	26	249	0.07	0.374
+size2.bam	PbANKA_12_v3	R	27	233	0.07	-0.893
+size2.bam	PbANKA_12_v3	R	28	225	0.07	-0.84
+size2.bam	PbANKA_12_v3	R	29	238	0.07	-0.787
+size2.bam	PbANKA_13_v3	F	19	39	0.42	1.879
+size2.bam	PbANKA_13_v3	F	20	27	0.42	1.049
+size2.bam	PbANKA_13_v3	F	21	33	0.42	0.966
+size2.bam	PbANKA_13_v3	F	22	27	0.42	0.136
+size2.bam	PbANKA_13_v3	F	23	23	0.42	-0.279
+size2.bam	PbANKA_13_v3	F	24	21	0.42	-1.607
+size2.bam	PbANKA_13_v3	F	25	24	0.42	-1.109
+size2.bam	PbANKA_13_v3	F	26	34	0.42	0.551
+size2.bam	PbANKA_13_v3	F	27	31	0.42	-0.03
+size2.bam	PbANKA_13_v3	F	28	22	0.42	-0.694
+size2.bam	PbANKA_13_v3	F	29	17	0.42	-0.86
+size2.bam	PbANKA_13_v3	R	19	48	0.42	1.879
+size2.bam	PbANKA_13_v3	R	20	50	0.42	1.049
+size2.bam	PbANKA_13_v3	R	21	43	0.42	0.966
+size2.bam	PbANKA_13_v3	R	22	39	0.42	0.136
+size2.bam	PbANKA_13_v3	R	23	38	0.42	-0.279
+size2.bam	PbANKA_13_v3	R	24	24	0.42	-1.607
+size2.bam	PbANKA_13_v3	R	25	27	0.42	-1.109
+size2.bam	PbANKA_13_v3	R	26	37	0.42	0.551
+size2.bam	PbANKA_13_v3	R	27	33	0.42	-0.03
+size2.bam	PbANKA_13_v3	R	28	34	0.42	-0.694
+size2.bam	PbANKA_13_v3	R	29	37	0.42	-0.86
+size2.bam	PbANKA_14_v3	F	19	35	0.49	0.764
+size2.bam	PbANKA_14_v3	F	20	30	0.49	0.524
+size2.bam	PbANKA_14_v3	F	21	38	0.49	2.085
+size2.bam	PbANKA_14_v3	F	22	39	0.49	0.884
+size2.bam	PbANKA_14_v3	F	23	32	0.49	-0.076
+size2.bam	PbANKA_14_v3	F	24	33	0.49	0.164
+size2.bam	PbANKA_14_v3	F	25	34	0.49	-0.917
+size2.bam	PbANKA_14_v3	F	26	31	0.49	-0.317
+size2.bam	PbANKA_14_v3	F	27	31	0.49	-0.797
+size2.bam	PbANKA_14_v3	F	28	27	0.49	-1.758
+size2.bam	PbANKA_14_v3	F	29	25	0.49	-0.557
+size2.bam	PbANKA_14_v3	R	19	37	0.49	0.764
+size2.bam	PbANKA_14_v3	R	20	40	0.49	0.524
+size2.bam	PbANKA_14_v3	R	21	45	0.49	2.085
+size2.bam	PbANKA_14_v3	R	22	34	0.49	0.884
+size2.bam	PbANKA_14_v3	R	23	33	0.49	-0.076
+size2.bam	PbANKA_14_v3	R	24	34	0.49	0.164
+size2.bam	PbANKA_14_v3	R	25	24	0.49	-0.917
+size2.bam	PbANKA_14_v3	R	26	32	0.49	-0.317
+size2.bam	PbANKA_14_v3	R	27	28	0.49	-0.797
+size2.bam	PbANKA_14_v3	R	28	24	0.49	-1.758
+size2.bam	PbANKA_14_v3	R	29	36	0.49	-0.557
+size2.bam	PbANKA_API_v3	F	19	22	0.55	0.68
+size2.bam	PbANKA_API_v3	F	20	22	0.55	0.564
+size2.bam	PbANKA_API_v3	F	21	35	0.55	0.796
+size2.bam	PbANKA_API_v3	F	22	43	0.55	1.608
+size2.bam	PbANKA_API_v3	F	23	30	0.55	0.854
+size2.bam	PbANKA_API_v3	F	24	21	0.55	0.042
+size2.bam	PbANKA_API_v3	F	25	29	0.55	0.332
+size2.bam	PbANKA_API_v3	F	26	13	0.55	-0.886
+size2.bam	PbANKA_API_v3	F	27	9	0.55	-1.292
+size2.bam	PbANKA_API_v3	F	28	6	0.55	-1.524
+size2.bam	PbANKA_API_v3	F	29	9	0.55	-1.176
+size2.bam	PbANKA_API_v3	R	19	29	0.55	0.68
+size2.bam	PbANKA_API_v3	R	20	27	0.55	0.564
+size2.bam	PbANKA_API_v3	R	21	18	0.55	0.796
+size2.bam	PbANKA_API_v3	R	22	24	0.55	1.608
+size2.bam	PbANKA_API_v3	R	23	24	0.55	0.854
+size2.bam	PbANKA_API_v3	R	24	19	0.55	0.042
+size2.bam	PbANKA_API_v3	R	25	16	0.55	0.332
+size2.bam	PbANKA_API_v3	R	26	11	0.55	-0.886
+size2.bam	PbANKA_API_v3	R	27	8	0.55	-1.292
+size2.bam	PbANKA_API_v3	R	28	7	0.55	-1.524
+size2.bam	PbANKA_API_v3	R	29	10	0.55	-1.176
+size2.bam	PbANKA_MIT_v3	F	19	12	0.67	1.059
+size2.bam	PbANKA_MIT_v3	F	20	14	0.67	1.525
+size2.bam	PbANKA_MIT_v3	F	21	11	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	F	22	15	0.67	0.36
+size2.bam	PbANKA_MIT_v3	F	23	5	0.67	-2.435
+size2.bam	PbANKA_MIT_v3	F	24	8	0.67	-0.572
+size2.bam	PbANKA_MIT_v3	F	25	13	0.67	0.593
+size2.bam	PbANKA_MIT_v3	F	26	13	0.67	0.593
+size2.bam	PbANKA_MIT_v3	F	27	10	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	F	28	12	0.67	-0.339
+size2.bam	PbANKA_MIT_v3	F	29	9	0.67	-0.572
+size2.bam	PbANKA_MIT_v3	R	19	9	0.67	1.059
+size2.bam	PbANKA_MIT_v3	R	20	9	0.67	1.525
+size2.bam	PbANKA_MIT_v3	R	21	5	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	R	22	3	0.67	0.36
+size2.bam	PbANKA_MIT_v3	R	23	1	0.67	-2.435
+size2.bam	PbANKA_MIT_v3	R	24	6	0.67	-0.572
+size2.bam	PbANKA_MIT_v3	R	25	6	0.67	0.593
+size2.bam	PbANKA_MIT_v3	R	26	6	0.67	0.593
+size2.bam	PbANKA_MIT_v3	R	27	6	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	R	28	3	0.67	-0.339
+size2.bam	PbANKA_MIT_v3	R	29	5	0.67	-0.572
Binary file test-data/size1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/size12.tab	Sat Oct 05 18:25:19 2019 -0400
@@ -0,0 +1,815 @@
+# Dataset	Chromosome	Polarity	Size	Counts	Strandness	z-score
+size1.bam	PbANKA_00_v3_archived_contig_1	F	19	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	20	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	21	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	22	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	23	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	24	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	25	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	26	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	27	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	28	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_1	F	29	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	19	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	20	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	21	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	22	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	23	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	24	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	25	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	26	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	27	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	28	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_2	F	29	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	19	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	20	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	21	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	22	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	23	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	24	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	25	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	26	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	27	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	28	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_3	F	29	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	19	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	20	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	21	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	22	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	23	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	24	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	25	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	26	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	27	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	28	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_4	F	29	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	19	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	20	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	21	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	22	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	23	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	24	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	25	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	26	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	27	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	28	0	2	0.0
+size1.bam	PbANKA_00_v3_archived_contig_5	F	29	0	2	0.0
+size1.bam	PbANKA_01_v3	F	19	3	0.46	1.768
+size1.bam	PbANKA_01_v3	F	20	4	0.46	0.795
+size1.bam	PbANKA_01_v3	F	21	2	0.46	-0.177
+size1.bam	PbANKA_01_v3	F	22	0	0.46	-0.663
+size1.bam	PbANKA_01_v3	F	23	2	0.46	1.282
+size1.bam	PbANKA_01_v3	F	24	4	0.46	0.795
+size1.bam	PbANKA_01_v3	F	25	2	0.46	-0.177
+size1.bam	PbANKA_01_v3	F	26	0	0.46	-0.663
+size1.bam	PbANKA_01_v3	F	27	0	0.46	-1.149
+size1.bam	PbANKA_01_v3	F	28	0	0.46	-0.177
+size1.bam	PbANKA_01_v3	F	29	0	0.46	-1.635
+size1.bam	PbANKA_01_v3	R	19	4	0.46	1.768
+size1.bam	PbANKA_01_v3	R	20	1	0.46	0.795
+size1.bam	PbANKA_01_v3	R	21	1	0.46	-0.177
+size1.bam	PbANKA_01_v3	R	22	2	0.46	-0.663
+size1.bam	PbANKA_01_v3	R	23	4	0.46	1.282
+size1.bam	PbANKA_01_v3	R	24	1	0.46	0.795
+size1.bam	PbANKA_01_v3	R	25	1	0.46	-0.177
+size1.bam	PbANKA_01_v3	R	26	2	0.46	-0.663
+size1.bam	PbANKA_01_v3	R	27	1	0.46	-1.149
+size1.bam	PbANKA_01_v3	R	28	3	0.46	-0.177
+size1.bam	PbANKA_01_v3	R	29	0	0.46	-1.635
+size1.bam	PbANKA_02_v3	F	19	7	0.54	2.83
+size1.bam	PbANKA_02_v3	F	20	5	0.54	-0.122
+size1.bam	PbANKA_02_v3	F	21	2	0.54	-0.122
+size1.bam	PbANKA_02_v3	F	22	3	0.54	-0.39
+size1.bam	PbANKA_02_v3	F	23	3	0.54	-0.39
+size1.bam	PbANKA_02_v3	F	24	2	0.54	-0.659
+size1.bam	PbANKA_02_v3	F	25	3	0.54	0.146
+size1.bam	PbANKA_02_v3	F	26	0	0.54	-1.464
+size1.bam	PbANKA_02_v3	F	27	4	0.54	0.146
+size1.bam	PbANKA_02_v3	F	28	4	0.54	0.146
+size1.bam	PbANKA_02_v3	F	29	5	0.54	-0.122
+size1.bam	PbANKA_02_v3	R	19	10	0.54	2.83
+size1.bam	PbANKA_02_v3	R	20	1	0.54	-0.122
+size1.bam	PbANKA_02_v3	R	21	4	0.54	-0.122
+size1.bam	PbANKA_02_v3	R	22	2	0.54	-0.39
+size1.bam	PbANKA_02_v3	R	23	2	0.54	-0.39
+size1.bam	PbANKA_02_v3	R	24	2	0.54	-0.659
+size1.bam	PbANKA_02_v3	R	25	4	0.54	0.146
+size1.bam	PbANKA_02_v3	R	26	1	0.54	-1.464
+size1.bam	PbANKA_02_v3	R	27	3	0.54	0.146
+size1.bam	PbANKA_02_v3	R	28	3	0.54	0.146
+size1.bam	PbANKA_02_v3	R	29	1	0.54	-0.122
+size1.bam	PbANKA_03_v3	F	19	4	0.39	0.815
+size1.bam	PbANKA_03_v3	F	20	4	0.39	1.232
+size1.bam	PbANKA_03_v3	F	21	5	0.39	-0.228
+size1.bam	PbANKA_03_v3	F	22	4	0.39	0.398
+size1.bam	PbANKA_03_v3	F	23	1	0.39	-0.228
+size1.bam	PbANKA_03_v3	F	24	5	0.39	-0.436
+size1.bam	PbANKA_03_v3	F	25	7	0.39	2.067
+size1.bam	PbANKA_03_v3	F	26	4	0.39	-0.228
+size1.bam	PbANKA_03_v3	F	27	1	0.39	-0.853
+size1.bam	PbANKA_03_v3	F	28	0	0.39	-1.062
+size1.bam	PbANKA_03_v3	F	29	0	0.39	-1.479
+size1.bam	PbANKA_03_v3	R	19	8	0.39	0.815
+size1.bam	PbANKA_03_v3	R	20	10	0.39	1.232
+size1.bam	PbANKA_03_v3	R	21	2	0.39	-0.228
+size1.bam	PbANKA_03_v3	R	22	6	0.39	0.398
+size1.bam	PbANKA_03_v3	R	23	6	0.39	-0.228
+size1.bam	PbANKA_03_v3	R	24	1	0.39	-0.436
+size1.bam	PbANKA_03_v3	R	25	11	0.39	2.067
+size1.bam	PbANKA_03_v3	R	26	3	0.39	-0.228
+size1.bam	PbANKA_03_v3	R	27	3	0.39	-0.853
+size1.bam	PbANKA_03_v3	R	28	3	0.39	-1.062
+size1.bam	PbANKA_03_v3	R	29	1	0.39	-1.479
+size1.bam	PbANKA_04_v3	F	19	2	0.46	-0.269
+size1.bam	PbANKA_04_v3	F	20	8	0.46	1.554
+size1.bam	PbANKA_04_v3	F	21	8	0.46	1.782
+size1.bam	PbANKA_04_v3	F	22	3	0.46	-0.497
+size1.bam	PbANKA_04_v3	F	23	7	0.46	1.098
+size1.bam	PbANKA_04_v3	F	24	3	0.46	-0.953
+size1.bam	PbANKA_04_v3	F	25	4	0.46	0.415
+size1.bam	PbANKA_04_v3	F	26	4	0.46	-0.953
+size1.bam	PbANKA_04_v3	F	27	5	0.46	-0.497
+size1.bam	PbANKA_04_v3	F	28	3	0.46	-1.181
+size1.bam	PbANKA_04_v3	F	29	5	0.46	-0.497
+size1.bam	PbANKA_04_v3	R	19	7	0.46	-0.269
+size1.bam	PbANKA_04_v3	R	20	9	0.46	1.554
+size1.bam	PbANKA_04_v3	R	21	10	0.46	1.782
+size1.bam	PbANKA_04_v3	R	22	5	0.46	-0.497
+size1.bam	PbANKA_04_v3	R	23	8	0.46	1.098
+size1.bam	PbANKA_04_v3	R	24	3	0.46	-0.953
+size1.bam	PbANKA_04_v3	R	25	8	0.46	0.415
+size1.bam	PbANKA_04_v3	R	26	2	0.46	-0.953
+size1.bam	PbANKA_04_v3	R	27	3	0.46	-0.497
+size1.bam	PbANKA_04_v3	R	28	2	0.46	-1.181
+size1.bam	PbANKA_04_v3	R	29	3	0.46	-0.497
+size1.bam	PbANKA_05_v3	F	19	3	0.1	0.62
+size1.bam	PbANKA_05_v3	F	20	8	0.1	0.979
+size1.bam	PbANKA_05_v3	F	21	8	0.1	0.261
+size1.bam	PbANKA_05_v3	F	22	5	0.1	1.578
+size1.bam	PbANKA_05_v3	F	23	3	0.1	-0.337
+size1.bam	PbANKA_05_v3	F	24	5	0.1	1.219
+size1.bam	PbANKA_05_v3	F	25	3	0.1	-1.175
+size1.bam	PbANKA_05_v3	F	26	7	0.1	0.022
+size1.bam	PbANKA_05_v3	F	27	5	0.1	-0.337
+size1.bam	PbANKA_05_v3	F	28	5	0.1	-1.415
+size1.bam	PbANKA_05_v3	F	29	3	0.1	-1.415
+size1.bam	PbANKA_05_v3	R	19	52	0.1	0.62
+size1.bam	PbANKA_05_v3	R	20	50	0.1	0.979
+size1.bam	PbANKA_05_v3	R	21	44	0.1	0.261
+size1.bam	PbANKA_05_v3	R	22	58	0.1	1.578
+size1.bam	PbANKA_05_v3	R	23	44	0.1	-0.337
+size1.bam	PbANKA_05_v3	R	24	55	0.1	1.219
+size1.bam	PbANKA_05_v3	R	25	37	0.1	-1.175
+size1.bam	PbANKA_05_v3	R	26	43	0.1	0.022
+size1.bam	PbANKA_05_v3	R	27	42	0.1	-0.337
+size1.bam	PbANKA_05_v3	R	28	33	0.1	-1.415
+size1.bam	PbANKA_05_v3	R	29	35	0.1	-1.415
+size1.bam	PbANKA_06_v3	F	19	11	0.11	0.854
+size1.bam	PbANKA_06_v3	F	20	3	0.11	0.042
+size1.bam	PbANKA_06_v3	F	21	10	0.11	0.158
+size1.bam	PbANKA_06_v3	F	22	8	0.11	1.781
+size1.bam	PbANKA_06_v3	F	23	7	0.11	0.738
+size1.bam	PbANKA_06_v3	F	24	7	0.11	0.854
+size1.bam	PbANKA_06_v3	F	25	5	0.11	-0.537
+size1.bam	PbANKA_06_v3	F	26	8	0.11	-1.233
+size1.bam	PbANKA_06_v3	F	27	6	0.11	-0.422
+size1.bam	PbANKA_06_v3	F	28	6	0.11	-0.306
+size1.bam	PbANKA_06_v3	F	29	3	0.11	-1.929
+size1.bam	PbANKA_06_v3	R	19	57	0.11	0.854
+size1.bam	PbANKA_06_v3	R	20	58	0.11	0.042
+size1.bam	PbANKA_06_v3	R	21	52	0.11	0.158
+size1.bam	PbANKA_06_v3	R	22	68	0.11	1.781
+size1.bam	PbANKA_06_v3	R	23	60	0.11	0.738
+size1.bam	PbANKA_06_v3	R	24	61	0.11	0.854
+size1.bam	PbANKA_06_v3	R	25	51	0.11	-0.537
+size1.bam	PbANKA_06_v3	R	26	42	0.11	-1.233
+size1.bam	PbANKA_06_v3	R	27	51	0.11	-0.422
+size1.bam	PbANKA_06_v3	R	28	52	0.11	-0.306
+size1.bam	PbANKA_06_v3	R	29	41	0.11	-1.929
+size1.bam	PbANKA_07_v3	F	19	10	0.04	-1.715
+size1.bam	PbANKA_07_v3	F	20	4	0.04	0.719
+size1.bam	PbANKA_07_v3	F	21	3	0.04	0.284
+size1.bam	PbANKA_07_v3	F	22	9	0.04	2.023
+size1.bam	PbANKA_07_v3	F	23	7	0.04	0.98
+size1.bam	PbANKA_07_v3	F	24	7	0.04	0.111
+size1.bam	PbANKA_07_v3	F	25	4	0.04	-0.237
+size1.bam	PbANKA_07_v3	F	26	1	0.04	-1.454
+size1.bam	PbANKA_07_v3	F	27	2	0.04	-0.411
+size1.bam	PbANKA_07_v3	F	28	2	0.04	-0.063
+size1.bam	PbANKA_07_v3	F	29	3	0.04	-0.237
+size1.bam	PbANKA_07_v3	R	19	84	0.04	-1.715
+size1.bam	PbANKA_07_v3	R	20	118	0.04	0.719
+size1.bam	PbANKA_07_v3	R	21	114	0.04	0.284
+size1.bam	PbANKA_07_v3	R	22	128	0.04	2.023
+size1.bam	PbANKA_07_v3	R	23	118	0.04	0.98
+size1.bam	PbANKA_07_v3	R	24	108	0.04	0.111
+size1.bam	PbANKA_07_v3	R	25	107	0.04	-0.237
+size1.bam	PbANKA_07_v3	R	26	96	0.04	-1.454
+size1.bam	PbANKA_07_v3	R	27	107	0.04	-0.411
+size1.bam	PbANKA_07_v3	R	28	111	0.04	-0.063
+size1.bam	PbANKA_07_v3	R	29	108	0.04	-0.237
+size1.bam	PbANKA_08_v3	F	19	6	0.37	0.358
+size1.bam	PbANKA_08_v3	F	20	13	0.37	1.626
+size1.bam	PbANKA_08_v3	F	21	4	0.37	1.203
+size1.bam	PbANKA_08_v3	F	22	9	0.37	0.499
+size1.bam	PbANKA_08_v3	F	23	7	0.37	0.64
+size1.bam	PbANKA_08_v3	F	24	8	0.37	-0.064
+size1.bam	PbANKA_08_v3	F	25	10	0.37	0.499
+size1.bam	PbANKA_08_v3	F	26	2	0.37	-0.909
+size1.bam	PbANKA_08_v3	F	27	8	0.37	-1.331
+size1.bam	PbANKA_08_v3	F	28	4	0.37	-1.05
+size1.bam	PbANKA_08_v3	F	29	4	0.37	-1.472
+size1.bam	PbANKA_08_v3	R	19	15	0.37	0.358
+size1.bam	PbANKA_08_v3	R	20	17	0.37	1.626
+size1.bam	PbANKA_08_v3	R	21	23	0.37	1.203
+size1.bam	PbANKA_08_v3	R	22	13	0.37	0.499
+size1.bam	PbANKA_08_v3	R	23	16	0.37	0.64
+size1.bam	PbANKA_08_v3	R	24	10	0.37	-0.064
+size1.bam	PbANKA_08_v3	R	25	12	0.37	0.499
+size1.bam	PbANKA_08_v3	R	26	10	0.37	-0.909
+size1.bam	PbANKA_08_v3	R	27	1	0.37	-1.331
+size1.bam	PbANKA_08_v3	R	28	7	0.37	-1.05
+size1.bam	PbANKA_08_v3	R	29	4	0.37	-1.472
+size1.bam	PbANKA_09_v3	F	19	11	0.53	1.46
+size1.bam	PbANKA_09_v3	F	20	16	0.53	0.872
+size1.bam	PbANKA_09_v3	F	21	9	0.53	0.481
+size1.bam	PbANKA_09_v3	F	22	11	0.53	0.481
+size1.bam	PbANKA_09_v3	F	23	13	0.53	1.068
+size1.bam	PbANKA_09_v3	F	24	7	0.53	-1.478
+size1.bam	PbANKA_09_v3	F	25	8	0.53	-0.89
+size1.bam	PbANKA_09_v3	F	26	12	0.53	-0.107
+size1.bam	PbANKA_09_v3	F	27	10	0.53	0.089
+size1.bam	PbANKA_09_v3	F	28	5	0.53	-1.87
+size1.bam	PbANKA_09_v3	F	29	11	0.53	-0.107
+size1.bam	PbANKA_09_v3	R	19	16	0.53	1.46
+size1.bam	PbANKA_09_v3	R	20	8	0.53	0.872
+size1.bam	PbANKA_09_v3	R	21	13	0.53	0.481
+size1.bam	PbANKA_09_v3	R	22	11	0.53	0.481
+size1.bam	PbANKA_09_v3	R	23	12	0.53	1.068
+size1.bam	PbANKA_09_v3	R	24	5	0.53	-1.478
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+size2.bam	PbANKA_14_v3	F	22	39	0.49	0.884
+size2.bam	PbANKA_14_v3	F	23	32	0.49	-0.076
+size2.bam	PbANKA_14_v3	F	24	33	0.49	0.164
+size2.bam	PbANKA_14_v3	F	25	34	0.49	-0.917
+size2.bam	PbANKA_14_v3	F	26	31	0.49	-0.317
+size2.bam	PbANKA_14_v3	F	27	31	0.49	-0.797
+size2.bam	PbANKA_14_v3	F	28	27	0.49	-1.758
+size2.bam	PbANKA_14_v3	F	29	25	0.49	-0.557
+size2.bam	PbANKA_14_v3	R	19	37	0.49	0.764
+size2.bam	PbANKA_14_v3	R	20	40	0.49	0.524
+size2.bam	PbANKA_14_v3	R	21	45	0.49	2.085
+size2.bam	PbANKA_14_v3	R	22	34	0.49	0.884
+size2.bam	PbANKA_14_v3	R	23	33	0.49	-0.076
+size2.bam	PbANKA_14_v3	R	24	34	0.49	0.164
+size2.bam	PbANKA_14_v3	R	25	24	0.49	-0.917
+size2.bam	PbANKA_14_v3	R	26	32	0.49	-0.317
+size2.bam	PbANKA_14_v3	R	27	28	0.49	-0.797
+size2.bam	PbANKA_14_v3	R	28	24	0.49	-1.758
+size2.bam	PbANKA_14_v3	R	29	36	0.49	-0.557
+size2.bam	PbANKA_API_v3	F	19	22	0.55	0.68
+size2.bam	PbANKA_API_v3	F	20	22	0.55	0.564
+size2.bam	PbANKA_API_v3	F	21	35	0.55	0.796
+size2.bam	PbANKA_API_v3	F	22	43	0.55	1.608
+size2.bam	PbANKA_API_v3	F	23	30	0.55	0.854
+size2.bam	PbANKA_API_v3	F	24	21	0.55	0.042
+size2.bam	PbANKA_API_v3	F	25	29	0.55	0.332
+size2.bam	PbANKA_API_v3	F	26	13	0.55	-0.886
+size2.bam	PbANKA_API_v3	F	27	9	0.55	-1.292
+size2.bam	PbANKA_API_v3	F	28	6	0.55	-1.524
+size2.bam	PbANKA_API_v3	F	29	9	0.55	-1.176
+size2.bam	PbANKA_API_v3	R	19	29	0.55	0.68
+size2.bam	PbANKA_API_v3	R	20	27	0.55	0.564
+size2.bam	PbANKA_API_v3	R	21	18	0.55	0.796
+size2.bam	PbANKA_API_v3	R	22	24	0.55	1.608
+size2.bam	PbANKA_API_v3	R	23	24	0.55	0.854
+size2.bam	PbANKA_API_v3	R	24	19	0.55	0.042
+size2.bam	PbANKA_API_v3	R	25	16	0.55	0.332
+size2.bam	PbANKA_API_v3	R	26	11	0.55	-0.886
+size2.bam	PbANKA_API_v3	R	27	8	0.55	-1.292
+size2.bam	PbANKA_API_v3	R	28	7	0.55	-1.524
+size2.bam	PbANKA_API_v3	R	29	10	0.55	-1.176
+size2.bam	PbANKA_MIT_v3	F	19	12	0.67	1.059
+size2.bam	PbANKA_MIT_v3	F	20	14	0.67	1.525
+size2.bam	PbANKA_MIT_v3	F	21	11	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	F	22	15	0.67	0.36
+size2.bam	PbANKA_MIT_v3	F	23	5	0.67	-2.435
+size2.bam	PbANKA_MIT_v3	F	24	8	0.67	-0.572
+size2.bam	PbANKA_MIT_v3	F	25	13	0.67	0.593
+size2.bam	PbANKA_MIT_v3	F	26	13	0.67	0.593
+size2.bam	PbANKA_MIT_v3	F	27	10	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	F	28	12	0.67	-0.339
+size2.bam	PbANKA_MIT_v3	F	29	9	0.67	-0.572
+size2.bam	PbANKA_MIT_v3	R	19	9	0.67	1.059
+size2.bam	PbANKA_MIT_v3	R	20	9	0.67	1.525
+size2.bam	PbANKA_MIT_v3	R	21	5	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	R	22	3	0.67	0.36
+size2.bam	PbANKA_MIT_v3	R	23	1	0.67	-2.435
+size2.bam	PbANKA_MIT_v3	R	24	6	0.67	-0.572
+size2.bam	PbANKA_MIT_v3	R	25	6	0.67	0.593
+size2.bam	PbANKA_MIT_v3	R	26	6	0.67	0.593
+size2.bam	PbANKA_MIT_v3	R	27	6	0.67	-0.106
+size2.bam	PbANKA_MIT_v3	R	28	3	0.67	-0.339
+size2.bam	PbANKA_MIT_v3	R	29	5	0.67	-0.572
Binary file test-data/size2.bam has changed