sometimes sample names clash

ben@u:~/git/graftM$ bin/graftM graft --graftm_package test/data/mcrA.gpkg/ --forward test/data/mcrA.gpkg/mcrA_1.1.fna test/data/mcrA.gpkg/mcrA_1.2.fna --output t --force; cat t/combined_count_table.txt 

                                GRAFT

                       Joel Boyd, Ben Woodcroft

                                                         __/__
                                                  ______|
          _- - _                         ________|      |_____/
           - -            -             |        |____/_
           - _     >>>>  -   >>>>   ____|          
          - _-  -         -             |      ______
             - _                        |_____|
           -                                  |______

06/05/2015 10:04:01 AM INFO: Working on mcrA_1
06/05/2015 10:04:01 AM INFO: Searching mcrA_1.1.fna
06/05/2015 10:04:01 AM INFO: 1 read(s) found
06/05/2015 10:04:01 AM INFO: Aligning reads to reference package database
06/05/2015 10:04:01 AM INFO: Working on mcrA_1
06/05/2015 10:04:01 AM INFO: Searching mcrA_1.2.fna
06/05/2015 10:04:01 AM INFO: 1 read(s) found
06/05/2015 10:04:01 AM INFO: Aligning reads to reference package database
06/05/2015 10:04:02 AM INFO: Placing reads into phylogenetic tree
06/05/2015 10:04:02 AM INFO: Placements finished
06/05/2015 10:04:02 AM INFO: Reading classifications
06/05/2015 10:04:02 AM INFO: Reads classified.
06/05/2015 10:04:02 AM INFO: Building summary table
06/05/2015 10:04:04 AM INFO: Building summary krona plot
06/05/2015 10:04:04 AM INFO: Cleaning up
06/05/2015 10:04:04 AM INFO: Done, thanks for using graftM!

#ID mcrA_1  ConsensusLineage
0   1   Root; mcrA; Euryarchaeota_mcrA; Methanomicrobia; Methanosarcinales; Methanosarcinaceae; Methanosarcina

There is two samples input, not one, so there should be two count columns.

@geronimp I'm working on #40 (biom) atm, so don't be tempted to fix just yet pls.

geronimp / graftM

sometimes sample names clash #58