karel-brinda/Phylign

Issues

• Add support for databases

  #268 opened 7 months ago by karel-brinda
  0

• Failed to run with custom data

  #265 opened 9 months ago by shenwei356
  4

• Tests are currently failing

  #258 opened 9 months ago by karel-brinda
  1

• LFS cluster mode: only snakemake 7.32.4 worked, 6.x or 8.x failed.

  #264 opened 9 months ago by shenwei356
  1

• make download has no option to download the whole 661K database.

  #262 opened 10 months ago by shenwei356
  1

• Add support for gzipped input files

  #259 opened 10 months ago by karel-brinda
  0

• ValueError: not enough values to unpack (expected 2, got 1)

  #256 opened 10 months ago by karel-brinda
  2

• Number of download threads reportedly being 1 on some machines regardless of the configuration

  #242 opened a year ago by karel-brinda
  12

• Trailing empty lines in the batches text file makes the pipeline fail

  #198 opened a year ago by leoisl
  9

• Zenodo is blocking some downloads

  #236 opened a year ago by leoisl
  20

• ANSI colors in Make Help command are not being interpreted

  #248 opened a year ago by Francii-B
  4

• COBS decompression dir disappeared from `config.yaml`

  #207 opened a year ago by karel-brinda
  5

• Fix max_download_threads in cluster mode

  #227 opened a year ago by leoisl
  2

• Decompressing COBS indexes takes way too much RAM

  #246 opened a year ago by leoisl
  1

• Add separate subcommands for downloading assemblies and cobs indexes

  #244 opened a year ago by Francii-B
  0

• Sometimes snakefmt breaks syntax for lambda functions

  #240 opened a year ago by karel-brinda
  0

• Downloading is not working and `make test` fails

  #234 opened a year ago by leoisl
  6

• Add a possibility to plug another mapper

  #231 opened a year ago by karel-brinda
  0

• batch_align.py loads up the whole query fasta into RAM

  #225 opened 2 years ago by leoisl
  2

• COBS postprocessing slower than COBS

  #178 opened 2 years ago by karel-brinda
  2

• When too many query/ref pairs are reported, final_stats uses too much of memory due to its naive Python implementation

  #185 opened 2 years ago by karel-brinda
  0

• Add a param for no filtration appended to COBS

  #187 opened 2 years ago by karel-brinda
  0

• Verifying memory consumption measurements

  #219 opened 2 years ago by karel-brinda
  8

• Minimap instances created even for 0 queries (COBS filtering not taken into account for mm2 instance building)

  #223 opened 2 years ago by karel-brinda
  2

• Read surprisingly non-matching the DB (cobs)

  #188 opened 2 years ago by karel-brinda
  38

• Separate benchmarks for individual steps of `make match` and `make map` (computation, then collection of results + filtering)

  #182 opened 2 years ago by karel-brinda
  0

• Mapping despite no candidates (probably)

  #190 opened 2 years ago by karel-brinda
  3

• End of year and my updates

  #221 opened 2 years ago by leoisl
  0

• When many cobs matches reported, batch_align uses an extremal amount of memory & swaps

  #183 opened 2 years ago by karel-brinda
  3

• Improve scripts/aggregate_sams.sh

  #201 opened 2 years ago by leoisl
  0

• Benchmarking ./scripts/aggregate_sams.sh doesn't involve compression, but this is the slowest part

  #209 opened 2 years ago by karel-brinda
  5

• Optimize result compression for time

  #216 opened 2 years ago by karel-brinda
  2

• For discussion - if no candidates for a minimap batch, report an empty alignment

  #189 opened 2 years ago by karel-brinda
  3

• Indexes are too large and thus are slowing down the pipeline significantly

  #203 opened 2 years ago by leoisl
  3

• Consider PAF as a possible output format

  #195 opened 2 years ago by karel-brinda
  1

• What's in reality the proportion of matching k-mers?

  #186 opened 2 years ago by karel-brinda
  3

• Unexpected swapping with COBS

  #181 opened 2 years ago by karel-brinda
  6

• Quick rejection of entire batches

  #194 opened 2 years ago by leoisl
  5

• Implement auto(N) for cobs_threads parameter

  #214 opened 2 years ago by leoisl
  2

• Unified data parameters table

  #211 opened 2 years ago by karel-brinda
  5

• Even with mem-stream the IO bottleneck seems to be partially present on OS X

  #208 opened 2 years ago by karel-brinda
  9

• Take into account xz decompression (`xzcat`) RAM usage when streaming

  #202 opened 2 years ago by leoisl
  11

• Number of COBS threads must be proportional to the RAM usage

  #206 opened 2 years ago by leoisl
  1

• Add LQ genomes to the dataset

  #196 opened 2 years ago by leoisl
  5

• Read names in tests are confusing and make debugging difficult

  #213 opened 2 years ago by karel-brinda
  1

• Implement index_load_mode parameter

  #204 opened 2 years ago by leoisl
  0

• Query results are being cut short

  #199 opened 2 years ago by leoisl
  0

• Load xzed file directly to COBS

  #197 opened 2 years ago by leoisl
  1

• Don't store SAM headers in the minimap output

  #179 opened 2 years ago by karel-brinda
  0

• Nothing is mapped on main branch

  #191 opened 2 years ago by leoisl
  1