Different results obtained using basealigncount() between the versions( 2.01 and 2.02.03)

[GoogleCodeExporter]

I used test.bed as input
chr1

1) What operating system are you using?
MacOS 10.7.5
2) What error message was displayed?
No error messages
3) What was the exact command you used that resulted in the error?
basealigncount(
   inputfile='data/test.bed',
   outputfile='data/test_2_02_03.basecount',
   extension=200,
   filetype='bed',
   twoBitFile='rn4.2bit' )
4) Please copy and paste any additional screen output that resulted from 
running the command
Importing reads from file /Users/NG10/data/test.bed ....
    Reads are formatted as bed ....
    Extending reads by 200 bp....
        For chr1 length is 267910886
        For chr1_random length is 3887217
        For chr2 length is 258207540
        For chr2_random length is 4341851
        For chr3 length is 171063335
        For chr3_random length is 1724363
        For chr4 length is 187126005
        For chr4_random length is 2124656
        For chr5 length is 173096209
        For chr5_random length is 2145107
        For chr6 length is 147636619
        For chr6_random length is 1770534
        For chr7 length is 143002779
        For chr7_random length is 1175105
        For chr8 length is 129041809
        For chr8_random length is 887087
        For chr9 length is 113440463
        For chr9_random length is 1166303
        For chrM length is 16300
        For chrX length is 160699376
        For chrX_random length is 1977738
        For chr10 length is 110718848
        For chr10_random length is 870782
        For chr11 length is 87759784
        For chr11_random length is 1278614
        For chr12 length is 46782294
        For chr12_random length is 953141
        For chr13 length is 111154910
        For chr13_random length is 608348
        For chr14 length is 112194335
        For chr14_random length is 1825095
        For chr15 length is 109758846
        For chr15_random length is 1609635
        For chr16 length is 90238779
        For chr16_random length is 1400107
        For chr17 length is 97296363
        For chr17_random length is 615889
        For chr18 length is 87265094
        For chr18_random length is 594525
        For chr19 length is 59218465
        For chr19_random length is 984116
        For chr20 length is 55268282
        For chr20_random length is 604928
        For chrUn length is 75822765
        For chrUn_random length is 6862066
        For chrUn_random length is 6862066
    Importing bed formatted reads
WARNING:  Less than 6 BED columns detected.  ZINBA expects exactly 6 BED 
columns (see ZINBA wiki for import file format)
    Skipped 1 reads
    Loaded 2 reads
    Sorting reads ...COMPLETE

Calculating counts at each base
Processing 2 reads
    Processing chr1..........
        Initializing length to 267910886
        2 reads mapped to chr1
        Printed results to data/test_2_02_03.basecount
-------- BASE ALIGN COUNTS COMPLETE SUCCESSFULLY --------

Original issue reported on code.google.com by mmiyajit...@gmail.com on 3 Oct 2012 at 5:47

[GoogleCodeExporter]

This is the rest part of the issue 35
input test.bed files:
chr1    101 300 test_1  0   +
chr1    501 700 test_2  0   +

summary of the result by version 2.01:
start   end count
1   100 0
101 300 1
301 500 0
501 700 1
701 last    0

summary of the result by version 2.02.03:
1   299 0
300 499 1
500 699 0
700 899 1
900 last    0

The result obtained using version2.02.03 seems miscalculation.

Original comment by mmiyajit...@gmail.com on 3 Oct 2012 at 6:08

[GoogleCodeExporter]

we are currently incorporating these issues into a new zinba version, check 
back soon for a comprehensive update

Original comment by homer...@gmail.com on 20 Nov 2012 at 8:54

• Changed state: Verified