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s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
https://s4hts.github.io/HTStream/
Apache License 2.0
49 stars 9 forks source link

Add concept of Tag to attach information to the read ids, needed for Primers and some future ideas. #216

Closed msettles closed 4 years ago

msettles commented 4 years ago

Tags are Sam style tags added to the read id when fastq, as columns 4 in single-end and 7/8 in paired-end reads.

Thought I had already merged this with master

msettles commented 4 years ago

The regression failure here I think is expected as the modified code changes the read ids adding information. Test fails running ../build/hts_Primers/hts_Primers output to hts_Primers.test zdiff hts_Primers.test.tab6.gz hts_Primers.tab6.gz 1,25c1,25

Which is the only app that incorporates my changes so far

msettles commented 4 years ago

The regression failure here I think is expected as the modified code changes the read ids adding information. Test fails running ../build/hts_Primers/hts_Primers output to hts_Primers.test zdiff hts_Primers.test.tab6.gz hts_Primers.tab6.gz 1,25c1,25

Which is the only app that incorporates my changes so far

Yes definitely expected, new tab format has 8 columns when tags are present, this is exactly what failed.

joe-angell commented 4 years ago

ok to fix regression:

cd regression
./regression.sh BUILD_DIR_PATH regen

then commit the changes

msettles commented 4 years ago

Fixed all requests merging