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Skip empty FASTA sequences, and allow to force taxids #27

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Skip empty FASTA sequences, and allow to force taxids #27

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This pull request includes two changes:

  • When observing a empty sequence, the program would exit in previous version. This is fixed. Additionally the number of empty sequences, and the number of sequences without valid taxonomy mapping, are counted and reported at the end.
  • Added the option -T to force set_lcas to set the taxid of the sequence as the taxid of its kmers - instead of the LCA. This proves very useful for re-setting the taxids of contaminant sequences after the database build.

fbreitwieser and others added 30 commits July 10, 2015 10:41
@fbreitwieser
Added .gitignore files
4487ec1
@fbreitwieser
Skip empty FASTA sequences instead of exiting the program
a07b9a2
@fbreitwieser
Added options -T to force taxid of the sequences, and -v for verbose …
d6071da 
…output

When -T is set, for each observed k-mer the taxid of the sequence is set - instead of the
lowest common ancestor of of the sequence taxid and the currently set taxid. This is useful
for setting the taxid of contaminant sequences, which may also be observed in database
genomes, to the contaminant taxid.

-v gives more verbose output
@fbreitwieser
added comments
14b74e2
@fbreitwieser
update
567ae7b
@fbreitwieser
Added '>kraken:taxid|' header parsing to set_lcas - makes it possible…
dfecb31 
… to run set_lcas on sequences that were not in the DB build originally
@fbreitwieser
Only report missing kmers when verbose
9fc61e3
@fbreitwieser
Use 'find ... -exec cat' instead 'find .. -print0 | xargs -0 cat'
c71ffbc
@fbreitwieser
Allow multiple --db arguments
8259c6a
@fbreitwieser
Count unique k-mers for each taxid
7c678d6
@fbreitwieser
Skip two gi2seqid and seqid2taxid map creation for now
3e5a009
@fbreitwieser
Don't display counts
93904c7
@fbreitwieser
Fix Makefile
905fa08
@fbreitwieser
Added taxdb from k-SLAM for writing report after classification
7b45304
@fbreitwieser
Build report and taxDB in Kraken
330e186
@fbreitwieser
Allow compressed output, and fix report file generation
c60b8a2
@fbreitwieser
Don't use nodes file in classify
aa6b179
@fbreitwieser
Added generate-taxonomy-ids-for-sequences and typed TaxonomyDB
0587b5e
@fbreitwieser
Use less critical pragma - better parallelization
06e7f7e
@fbreitwieser
Fix for using multiple databases for search
ff63944
@fbreitwieser
Update README.md
6476863
@fbreitwieser
Do not need taxonomy nodes anymore
8f4b184
@fbreitwieser
Check if there's a taxonomy entry
77cac13
@fbreitwieser
Merge branch 'taxid-bitmap' of https://github.com/fbreitwieser/kraken …
56c5872 
…into taxid-bitmap

Conflicts:
	src/taxdb.h
@fbreitwieser
Merge branch 'master' of https://github.com/fbreitwieser/kraken
4073388
@fbreitwieser
Use template for ReadCounts
dcaec29
@fbreitwieser
Merge branch 'taxid-bitmap'
2ddf645
@fbreitwieser
Renamed to kraken_hll
53560de
@fbreitwieser
Fixed building of kraken_hll
c6cf5bc
@fbreitwieser
Update README.md
e76de48
@fbreitwieser
Allow to run build_taxdb with a taxdb as consistency check
2172caa
@fbreitwieser
Update to classification grading
eb9447e
@fbreitwieser
Do not give separate taxids for human sequences (fixed now)
75b24ae
@fbreitwieser
Add species subgroup and group ranks
f15112d
@fbreitwieser
Don't use .at() for vector access
3090304
@fbreitwieser
Test modification of lca
9c11d87
@fbreitwieser
Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll
cdc9fb6 
* 'master' of https://github.com/fbreitwieser/kraken-hll:
  Dump taxdb without ending separators (for kraken-report)
@fbreitwieser
Update
7d1ab24
@fbreitwieser
Update
5ea9f06
@fbreitwieser
Many small changes to make it working for GCC 4.4 / C++0x
970c4ca
@fbreitwieser
Make sure TaxDB is not copied
d5b8dc2
@fbreitwieser
Fox parent map generation in taxDB
16813a7
@fbreitwieser
Add environment CPPFLAGS and LDFLAGS
7466810
@fbreitwieser
Change name to KrakenHLL
dd7fc4f
@fbreitwieser
Change name to KrakenHLL
0c33f0e
@fbreitwieser
Update
274e41f
@fbreitwieser
Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll
fadae7b 
* 'master' of https://github.com/fbreitwieser/kraken-hll:
  Change name to KrakenHLL
  Add environment CPPFLAGS and LDFLAGS
  Fox parent map generation in taxDB
  Make sure TaxDB is not copied
  Many small changes to make it working for GCC 4.4 / C++0x

Conflicts:
	tests/build-dbs.sh
@fbreitwieser
Create taxDB if not present
69d8352
@fbreitwieser
Compute k-mer counts if not present
d83c579
@fbreitwieser
Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll
96ecc4b 
* 'master' of https://github.com/fbreitwieser/kraken-hll:
  Update
  Change name to KrakenHLL

Conflicts:
	install_kraken.sh
	tests/build-dbs.sh
	tests/test-on-simulated-reads.sh
@fbreitwieser
Fix indent
30a6538
@fbreitwieser
Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll
4e3cbd3 
* 'master' of https://github.com/fbreitwieser/kraken-hll:
  Compute k-mer counts if not present
  Create taxDB if not present
  Update
  Change name to KrakenHLL
@fbreitwieser
Fix gzstream compilation, update on HLL
f34f8d4
@fbreitwieser
Fix gzstream building and licensing
93c155f
@fbreitwieser
Fix licensing
c6871c1
@fbreitwieser
Merge branch 'master' of https://github.com/fbreitwieser/kraken-hll
e4904a7 
* 'master' of https://github.com/fbreitwieser/kraken-hll:
  Fix gzstream building and licensing
  Fix gzstream compilation, update on HLL

Conflicts:
	src/hyperloglogplus.h
@fbreitwieser
Fix taxonomy reporting order and percentage
53314ae
@fbreitwieser
Fixed HLL bug introduced by using vector for sparse representation
10f5998
@fbreitwieser
Fix Makefile
1d37b54
@fbreitwieser
Allow setting custom precision
a95bd85
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