Edit distance txt files have 0 counts for all values

[ivelsko]

Hi DamageProfiler team,

I'm getting edit distance txt files that have 0 values for all edit distances, while the edit distance pdf and svg files show bar plots with total read counts that match the total counts in the length distribution and damage plots. The runs all complete successfully and I can't find an error.

I can't find any reference to edit distance in the issues here, but is this a known issue, and is there anything I can do to get the txt file to have the actual counts? The edit distance files look like this

#Edit distances for file:MID072.A0101.Tf.mapped_q25l30_rmdup.bam
Edit distance	Occurrences
0.0	0
1.0	0
2.0	0
4.0	0
8.0	0
5.0	0
3.0	0
6.0	0
7.0	0

While the corresponding pdf isn't all 0 occurences:
edit_distance.pdf

And the length distribution file has read counts

# table produced by DamageProfiler
# using mapped file MID072.A0101.Tf.mapped_q25l30_rmdup.bam
# Sample ID: MID072.A0101.Tf.mapped_q25l30_rmdup.bam
# Std: strand of reads
Std	Length	Occurrences
+	30	4076
+	31	4426
+	32	4767
+	33	5060
+	34	5176
+	35	5316

etc

And the log file is

2023-11-30 13:03:44 INFO  StartCalculations:101 - Welcome to DamageProfiler v1.1

2023-11-30 13:03:44 INFO  StartCalculations:104 - Parameters: 

2023-11-30 13:03:44 INFO  StartCalculations:105 - 	Analysis of file (-i):		MID072.A0101.Tf.mapped_q25l30_rmdup.bam
2023-11-30 13:03:44 INFO  StartCalculations:106 - 	Output folder (-o):		null
2023-11-30 13:03:44 INFO  StartCalculations:107 - 	Reference (-r, optional):	
2023-11-30 13:03:44 INFO  StartCalculations:108 - 	Species (-s, optional):		null
2023-11-30 13:03:44 INFO  StartCalculations:109 - 	Species list (-sf, optional):	null
2023-11-30 13:03:44 INFO  StartCalculations:110 - 	Length (-l):			100
2023-11-30 13:03:44 INFO  StartCalculations:111 - 	Threshold (-t):			25
2023-11-30 13:03:44 INFO  StartCalculations:112 - 	Height y-axis (-yaxis):		0.4
2023-11-30 13:03:44 INFO  StartCalculations:113 - 	Color C->T:			0xff0000ff
2023-11-30 13:03:44 INFO  StartCalculations:114 - 	Color G->A:			0x0000ffff
2023-11-30 13:03:44 INFO  StartCalculations:115 - 	Color insertions:		0xff00ffff
2023-11-30 13:03:44 INFO  StartCalculations:116 - 	Color deletions:		0x008000ff
2023-11-30 13:03:44 INFO  StartCalculations:117 - 	Color other:			0x808080ff
2023-11-30 13:03:44 INFO  StartCalculations:118 - 	Title:				MID072.A0101.Tf.mapped_q25l30_rmdup
2023-11-30 13:03:44 INFO  StartCalculations:119 - 	ssLib protocol used:		false
2023-11-30 13:03:44 INFO  StartCalculations:120 - 	Use only merged reads:		false

2023-11-30 13:03:44 INFO  StartCalculations:179 - Starting analysis

2023-11-30 13:03:44 INFO  StartCalculations:65 - 	Reading file MID072.A0101.Tf.mapped_q25l30_rmdup.bam
2023-11-30 13:03:44 INFO  StartCalculations:108 - 	Start processing each mapped record in input file
2023-11-30 13:03:52 INFO  StartCalculations:914 - 	Base frequencies are normalized

2023-11-30 13:03:52 INFO  StartCalculations:104 - Start writing output files:
2023-11-30 13:03:52 INFO  StartCalculations:149 - 	lgdistribution.txt
2023-11-30 13:03:52 INFO  StartCalculations:535 - 	3pGtoA_freq.txt and 5pCtoT_freq.txt
2023-11-30 13:03:52 INFO  StartCalculations:322 - 	misincorporation.txt
2023-11-30 13:03:53 INFO  StartCalculations:243 - 	DNA_composition_sample.txt
2023-11-30 13:03:53 INFO  StartCalculations:208 - 	DNA_comp_genome.txt
2023-11-30 13:03:53 INFO  StartCalculations:634 - 	5p_freq_misincorporations.txt and 3p_freq_misincorporations.txt
2023-11-30 13:03:53 INFO  StartCalculations:117 - 	dmgprof.json
2023-11-30 13:03:53 INFO  StartCalculations:933 - 	DamagePlot_three_prime.svg, DamagePlot.pdf, and DamagePlot_five_prime.svg
2023-11-30 13:03:59 INFO  StartCalculations:494 - 	Length_plot.pdf, Length_plot_combined_data.svg, and Length_plot_forward_reverse_separated.svg
2023-11-30 13:03:59 INFO  StartCalculations:518 - 	edit_distance.pdf and edit_distance.svg
2023-11-30 13:03:59 INFO  StartCalculations:772 - 	editDistance.txt

2023-11-30 13:03:59 INFO  StartCalculations:195 - Statistics:
2023-11-30 13:03:59 INFO  StartCalculations:196 - 	# of total reads in input file:		594,393
2023-11-30 13:03:59 INFO  StartCalculations:197 - 	# reads used for damage calculation:	594,393 (100.0%)

2023-11-30 13:03:59 INFO  StartCalculations:200 - 	Length distribution:
2023-11-30 13:03:59 INFO  StartCalculations:201 - 		- mean		63.71
2023-11-30 13:03:59 INFO  StartCalculations:202 - 		- median	60
2023-11-30 13:03:59 INFO  StartCalculations:203 - 		- std		24.16


2023-11-30 13:03:59 INFO  StartCalculations:205 - FINISHED SUCCESSFULLY: Output files generated and saved: out/MID072.A0101.Tf.mapped_q25l30_rmdup
2023-11-30 13:03:59 INFO  StartCalculations:232 - Runtime of DamageProfiler:	15.13 seconds

I submitted the run with

java -jar DamageProfiler-1.1-java11.jar \
        -i MID072.A0101.Tf.mapped_q25l30_rmdup.bam \
        -o out/MID072.A0101.Tf.mapped_q25l30_rmdup

Thanks,
Irina