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…command line; also changes output
…nger than alignment
Update generate_site_positions.py
…riate place; bug fix in countligations for stem
This is a complete rewrite of generate_site_positions.py. The new version runs under python3 as well as python2. It corrects an error found in the previous version where the very last number in the result was wrong (it was one too many). It can work with multiple test strings at the same time (they must be enumerated in a python list). Wildcard search (using N, M, R, W, Y, S, K, H, B, V, D) is also possible with the new algorithm. Compared to the previous version this program runs faster for simple test strings (strings without wildcards). The script contains a dictionary for genome/filename mappings and another one for enzyme/test string mappings which users can modify easily according to their needs.
When there is no 50 bp bin with 1000 or more counts, the awk command failed to create the "sum" variable, so "bins1000" was NULL. I added a condition for this awk command to return 0 when this happens.
Update calculate_map_resolution.sh
Enable multithreading option for "bwa aln"
multithreading for "bwa aln"
Added a check were if ligation is a regex, and unquoted, then add quotes. Removed quotes from count_ligation.sh
Fixed issues with multiple ligation, add Arima ligation
A complete rewrite of generate_site_positions.py
…was not doing the right thing
Major: - BWA now aligns in paired end mode. This requires BWA version 0.7.17 or higher; short read and short end mode are now deprecated Minor: - The chimera handling script now includes the header and prints out tab-delimited, for better conversion to BAM; it also no longer looks for the /1, /2 but rather looks for the SAM flag - We dedup collisions now - An addition to the dups script makes it run faster and with less memory when there are a lot of duplicates - Statistics updated in CPU to properly handle multiple ligations; also added scripts in CPU that were missing for mega - Made the names correct in the stats_sub script - Count ligations explicitly excludes the readname in the fastq file
…ace difference in split_rmdups.awk. Dups.awk now the same as rest of Juicer, with additional code block to exit out of loop when second read end gets too far away.
…icer versions, made fragment delimited maps no longer the default; can include via the -f flag
suppress too many args error if host returns >1 line
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