maintain sample order in GEM output

[hharg910]

Conserve Sample Order

The order of the samples in the GEM files is different across the different GEM types. For example, in the raw GEM the sample order is S_05, S_02, S_03, S_01, S_04. But in the TPM Gem, the sample order is S_01, S_03, S_05, S_04, S_02. While not inherently an issue, this is inconvenient when using GEMs for downstream analyses that might require the sample ID headers to be converted. Is it possible to conserve the order of samples across each GEM produced by a read mapping experiment?