.bam files originated from .bedpe as input

First of all, many thanks for developing this amazing tool.

I have been used without problems for single-end reads, however, I 'm receiving the following error when I try to use for .bam files originated from .bedpe files.

The error:

$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper$ ngs.plot.r -G hg19 -R genebody -C config_ngsplot.txt -O metaplot_HiCHIPxHiCxChIPseq -L 5000
Configuring variables...
Using database:
~/Desktop/Software/ngsplot-develop/database/hg19/hg19.ensembl.genebody.protein_coding.RData
Done
Loading R libraries.....Done
Analyze bam files and calculate coverageopen: No such file or directory
Error in FUN(X[[i]], ...) : failed to open SAM/BAM file
  file: '~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper/Hi-C-Input_sorteds_interaction.bam'
Calls: headerIndexBam ... indexBam -> sapply -> sapply -> lapply -> FUN -> .Call
Execution halted
$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper

this is the file

$:~/Desktop/Software/HiChipper/HiCPro_PE_norm_hichipper$ samtools view Hi-C-Input_sorted_interaction.bam | head
NB500931:198:HGYHWBGX7:4:23404:14256:4594   179 chr1    74395   0   74M chr12   128326315   0   TTTGGGGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGT  EAEAEEEEEEAEEAEE<EE<AEEEEEEEEEEAEEEEEEEEE<EEEEEEEEEEEEAAEEEEE6EAEEEEAAAAAA  AS:i:-15    XN:i:0  XM:i:3  XO:i:0  XG:i:0  NM:i:3  MD:Z:0G2C1A68   YT:Z:UU RG:Z:BMG    CT:Z:VI
NB500931:198:HGYHWBGX7:4:11608:25382:13700  131 chr1    247762  32  74M chr20   8107332 0   GATCACTTGAGACCAGGAGTTCGCAACCAGCCTGGACAACATAGGGAGACTCCATCTCCACACATGCCAAAAAA  A6A6A/EEEEE/EAA/EEEE/EEEEEEE6EEE/EEAE/EEEEEEEEEE/AEAA///E/E/E<AAAEEEE/EAAE  AS:i:0  XS:i:-5 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:74 YT:Z:UU RG:Z:BMG    CT:Z:VI
NB500931:198:HGYHWBGX7:1:11307:24219:17516  163 chr1    526530  32  75M chr8    274191  0   AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTCAGCCATACAGAGGAATGACAGC AAAAAEEEEEEEEAEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEAEAEAEA/EEA/ AS:i:0  XS:i:-5 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:75 YT:Z:UU RG:Z:BMG    CT:Z:VI
NB500931:198:HGYHWBGX7:1:12204:22942:17653  163 chr1    526530  0   75M chr8    274191  0   AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTGAGCCCGACAGCGGAATGACAGC AAA6AEEA66EEE///E/EE//AEAE/E6EEE/E/////AA//6E/E/E//E//<E///E/EAEAE/E/E/EE// AS:i:-14    XN:i:0  XM:i:4  XO:i:0  XG:i:0  NM:i:4  MD:Z:52C4A0T4A11    YT:Z:UU RG:Z:BMG    CT:Z:VI
NB500931:198:HGYHWBGX7:1:21212:19707:11556  163 chr1    526530  15  75M chr8    274191  0   AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTCCGCCATACAGAGGAATGACAGC A/6AA/AA//AEE/EE/EEAE6/EAEAEE/6EE//E/E//EEEEEAEAAE/EE/A/EEEE/EAEEAE/EEEAE// AS:i:-3 XS:i:-8 XN:i:0  XM:i:1  XO:i:0  XG:i:0  NM:i:1  MD:Z:53A21  YT:Z:UU RG:Z:BMG    CT:Z:VI
NB500931:198:HGYHWBGX7:1:22311:6282:13191   99  chr1    526530  31  75M chr8    274191  0   AGCGGATGATGGATAAACAGAACGTGGTGTGTATACACAGTGGAATATTCTTCAGCCATACAGAGGAATGACAGC /AAAAEA/EAEAEAEEEEE/EEEEAEAE/EE6EEEAEAEEE</A///<EEEEE<AEEEAAEEEEEEAEE/EE/EE AS:i:0  XS:i:-4 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:75 YT:Z:UU RG:Z:BMG    CT:Z:VI

I saw this closed thread https://github.com/shenlab-sinai/ngsplot/issues/9, but not sure if it applies to my case.

Is there a way to use this type of file as input?

Many thanks,

Raphael

shenlab-sinai / ngsplot

.bam files originated from .bedpe as input #83