"ANNOTATION_MAPPING Combined" does not accept valid READ_DESCRIPTOR parameter

[GoogleCodeExporter]

i'm running the flux (1.0-RC1):

/users/rg/jlagarde/Flux-Capacitor-1.0-RC1/bin/flux -f -t capacitor -p 
LID9207.cshl_caltech_Ap_incl_in_longv7_intergenic.star_flux_paramfile.txt

here's the content of the param file:
#####
ANNOTATION_FILE 
/users/rg/sdjebali/ENCODE_AWG/Analyses/Cufflinks_models/cshl_caltech_Ap_incl_in_
longv7_intergenic.gtf
MAPPING_FILE ./bed/LID9207.star_mapping_forflux_sorted_ok.bed.gz
STDOUT_FILE 
/users/rg/jlagarde/projects/encode/scaling/whole_genome/analysis/flux_capacitor/
cshl//flux_out/LID9207.cshl_caltech_Ap_incl_in_longv7_intergenic.cshl_caltech_Ap
_incl_in_longv7_intergenic.gtf
TMP_DIR /users/rg/jlagarde/temp/flux/
READ_DESCRIPTOR MATE2_SENSE
ANNOTATION_MAPPING Combined
SORT_IN_RAM true
#####

It outputs nothing, and here's what it errputs:

#####
[INFO] I am the Flux Toolbox ( Devel Mode ), nice to meet you!

[PRE-CHECK] I am checking availability of the required lpsolve JNI libs.
[PRE-CHECK]     * successfully loaded lpsolve JNI (version 5.5,release 0,build 
14)

[ERROR] Unable to load settings from 
LID9207.cshl_caltech_Ap_incl_in_longv7_intergenic.star_flux_paramfile.txt

 Annotation mapping COMBINED requires a read descriptor MATE1_SENSE or MATE2_SENSE!
#####

which doesn't make sense, right?

Original issue reported on code.google.com by gmicha@gmail.com on 29 Sep 2011 at 11:32

[GoogleCodeExporter]

able to reconstruct the issue

Original comment by gmicha@gmail.com on 29 Sep 2011 at 12:10

• Changed state: Accepted

[GoogleCodeExporter]

Fixed string comparison in parameter validator

Original comment by gmicha@gmail.com on 30 Sep 2011 at 10:54

• Changed state: Fixed
• Added labels: Capacitor