fermi-lite

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Fermi-lite aggressive trimming

1

Hi, When setting aggressive trimming in fermi-lite to pop bubbles in heterozygous regions, what is the strategy being employed. Is the longer path in the bubble being kept or the...

cgroza

mr-c

by replacing some legacy `__sync` operations with their `__atomic` equivalents

mr-c

bseq1_t --> fseq1_t

3

Hi Heng, In trying to link bwa and fml in the same executable, I ran into an issue where ``bseq1_t`` was defined differently in each library. I ended up making...

walaj

Avoid name space conflict with bwa

1

This addresses https://github.com/lh3/fermi-lite/issues/5

tillea

Hi, I'm just opening this issue to link to a pull request which adds an enhancement of [libSeqLib](https://github.com/walaj/SeqLib). If this patch would be applied libSeqLib could drop the incompatible code...

tillea

Consider the following 8 reads. ``` >seq1 ATCCTGAGAATCAATCTGTGAAAATTATGTCTTGGGAGGAGGGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTC >seq2 GGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATCTCACAGAATCGCAAAGGAAGAAAATCAGGGCCTA >seq3 TTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAATCGCAAAGGAAGAAAATCAGGGCCTACCTATCTAAATTTAAAATT >seq4 GAAATTTTAAATTTAGATATGTAGGCCCTGATTTTCTTCCTTTGCGATTCTGTGATATTCAAGACCTGCTTCTAGATAGCTAAGAGTTCCAGCTTTTCTA >seq5 TGAGAAAATTATGTCTTGGGAGGAGGGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAAT >seq6 TGAAAATTATGTCTTGGGAGGAGGGGAAGGAAACCAAAAATTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAATCG >seq7 TTTTTAGAAAAGCTGGAACTCTTAGCTATCTAGAAGCAGGTCTTGAATATCACAGAATCGCAAAGGAAGAAAATCAGGGCCTACATATCTAAATTTAAAA >seq8 ATAGCTAAGAGTTCCAGCTTTTCTAAAAATTTTTGGTTTCCTTCCCCTCCTCCCAAGACATAATTTTCACAGATTGATTCTCAGGATTGGCAATCATGCA ``` A quick multiple sequence alignment shows that...

standage

No assembly reported for 100 reads with the same sequence

8

@lh3 I was playing around with this tool but I couldn't get it to work on a "simple" case. I duplicated a read 100 times and would expect it to...

nh13

expose min_elen as a command line option

2

https://github.com/lh3/fermi-lite/issues/7

nh13

Remove need for SSE2 support

3

Currently the code in `ksw.c` seems to need SSE2 to compile. It would be nice to have some kind of -- probably slower -- fallback implementation to improve support on...

satta