Inconsistent file names or a bug?

[mtop]

I just ran the code on a new dataset and found that a read pair ended up in both the "mapping_full_.sam" and the "non_mappers_.sam" files. Judging from the filename convention, this looks like an unexpected result. Bug?

[mtop@albiorix raw_data_to_no-skeletonema-016536_2015_10_09]$ pwd
/nobackup/data5/Skeletonema_marinoi_genome_project/test/Anja_Kamps_data/mapping_to_016536/raw_data_to_no-skeletonema-016536_2015_10_09
[mtop@albiorix raw_data_to_no-skeletonema-016536_2015_10_09]$ head -300 mapping_full_2015_10_09.sam | tail -1 | cut -f 1
M03388:4:000000000-AD033:1:1101:10080:1052
[mtop@albiorix raw_data_to_no-skeletonema-016536_2015_10_09]$ grep "M03388:4:000000000-AD033:1:1101:10080:1052" non_mappers_2015_10_09.sam 
M03388:4:000000000-AD033:1:1101:10080:1052  77  *   0   0   *   *   0   0   GTCCATCGTGGGAACAAGGAGATTTGAAAAGTCGAGGCGTTCGCCCTTTGGATATGTCNAATGTGGAGGCTTCCACTTCTCCCATTCTCCACTTNNTGNNTCNACANNGTACTCAAAGATTGTTTCCCNCTCNNCNACNTTTGNCNTNNCCGNAGGANNACGTNNNCNNNGCCANNNANCAAANNNCATNCNGTCTTCCNCTNCNNGCAATGCTCCANCACTCCNACAGAGACANNNNACAAATACTCGTTCCAATGCCACANNCNATGTNNANGTNNNNNNNNTNNNNTCNNNNCCTTC    CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGDGGGG#:CFGGGGGGGGGGGCDGGFCAFGGFGGGGGFAFGG##::##::#::<##::BFGGGGGEFEGFDFFGGG#4:?##+#::#:AB<#8#8##88A#33A3##68=+###8###8+8@###+#86:B###66@#3#4=DFFFF#14#4##44=CG6D=CC*#*2=CFF#27/9CF7C*####210*29+:8FEFFFFGFFF??)?5##,#---.##-#(-########(####(,####(,--(    YT:Z:UP YF:Z:NS
M03388:4:000000000-AD033:1:1101:10080:1052  141 *   0   0   *   *   0   0   NTACTCGATGATAACAAGATCTNNACGCTTGCCAATGGNNANCGCNNCCCCNTGACAGACNATGTCNAGNTTATGTTTGAAGTTNAAACGCTTGTGAATGCATCTCCAGCTACGGTATCCCGAGCTGGAATTNNTNATGTAAGTNACNCNNATNNGGNTTGGTGNNCNNTATTGGANGCNTNGGTGCGAAAGAGACCNNNNCNTGATCGACNNNNNNNGTTNAGANNCCNNNTTGAGAANNNNNCAGGCAATAGCCCCGCNNNNAATCCCNGNCCATGATTTACCCTCTTCCAGCAAAATA   #86BCCGCCFECE,EFED8F<F##9=CFGGGGFCGFG8##,#::D##,9,C#:C<,9CED#66CFF#,9#:,@CFD9CEFFG@9#:B7FGG>FGE<<55,:EA9AF99FA<<?C,A99EFEEC@=+4EFGFG##9#+9>D>FEF#+8#8##+6##66#66>83+##6##++6A=,,#5+#4#5+@1@>9*;@799D9####*#*33*/?))#######)0/#)2.##).###.(2).2A#####,(--216()6<).((-####(,(-()#-#--48())6<)).(4((.).)6.(,((-.   YT:Z:UP YF:Z:NS

[mtop]

Which of these files:

[mtop@albiorix lists]$ ls
raw_data_to_no-skeletonema-016536_half_mappers.lst  raw_data_to_no-skeletonema-016536_non_mapper.lst
raw_data_to_no-skeletonema-016536_mapper.lst

...corresponds to the directories "half_mapped_reads", "mapped_reads" and "non_mapped_reads"? I suggest the files and directories are renamed in a more consistent way.