pseudo mode:

• A new mode kallisto pseudo has been implemented which allows reads to only be pseudoaligned. This mode is useful during single cell analysis as many different experiments (single cells) can be analyzed at the same time and their equivalence classes will be consistent. It will also output a matrix of equivalence class counts (as used in Fast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts).

Bug fixes:

• Fixes a segfault when running quant in --bias mode
• Fixes a small error in allocation of memory
• Ensures that single-end reads have reasonable length mappings when mapping to short transcripts