HTStream
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s4hts
A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
UMIs in known location in a read, extract and use as part of tag
Sam output is supported, also support sam input, requires storing reads in pairs until the pair is found. Related to #101
single file inputs are fine, but if multiple files are input with commas for reads 1 and 2 it will not run: Unhandled Exception: File 00-RawData/41_S15_L001_R1_001.fastq.gz,00-RawData/41_S15_L002_R1_001.fastq.gz,00-RawData/41_S15_L003_R1_001.fastq.gz was not found
Currently adapter trimmer employs the same algorithm as overlapper and will check for ALL overlaps short and long. However, the way the alg works its not an easy change, this...
All Mac versions that I can find are HTStream 1.1.0, which differs in substantial ways from version 1.3.0 and causes scripts designed for the newer version unusable.
So this PR has a number of changes. 1. Additional parameters for EU (specifies separator for PE reads, optionally add UMI as a tag similar to primers) and SD (specifies...
