lastz/lastz issues and pull requests

#63 - avoid requiring score type to be escaped at compile-time

Pull Request - State: open - Opened by jfgrimm 29 days ago - 3 comments

#62 - nameparse specifiers do not work for 2bit files

Issue - State: open - Opened by rsharris 29 days ago

#60 - Clarifications Needed on blastn Output Format and LASTZ Functionality for Hit Identification

Issue - State: open - Opened by Salihmaya 9 months ago - 2 comments

#59 - Confusion about the multiple arguements in target

Issue - State: open - Opened by 981Hao 10 months ago - 2 comments

#58 - Support for gzip files

Issue - State: open - Opened by yatisht about 1 year ago - 20 comments

#57 - Where are all the temporary files stored?

Issue - State: open - Opened by chenyangkang over 1 year ago - 3 comments

#56 - Reported score sometimes penalizes for an extra gap open.

Issue - State: open - Opened by rsharris over 1 year ago

#55 - how to use multiple threads in aligning

Issue - State: open - Opened by tinyfallen over 1 year ago - 7 comments

#54 - What is target and query, and -seed=half7 vs --seed=match7 discrepancies

Issue - State: open - Opened by MichaelHiller over 1 year ago - 13 comments

#53 - In add_segment(), table size exceeds allocation limit

Issue - State: open - Opened by rsharris almost 2 years ago - 5 comments

#52 - --allocate:traceback 1.99G is not enough for some chromosome aligning

Issue - State: open - Opened by yr-gh almost 2 years ago - 5 comments

#51 - different results between lastz and blast

Issue - State: closed - Opened by gorliver about 2 years ago - 12 comments

#50 - Output unaligned sequences

Issue - State: open - Opened by damiankao about 2 years ago - 1 comment

#49 - Inconsistencies using --self --nomirror with --strand=minus

Issue - State: closed - Opened by rsharris over 2 years ago - 1 comment

#48 - Suggestion for efficiency

Issue - State: open - Opened by mlcossette9224 over 2 years ago - 3 comments

#47 - LastZ_32 is taking a long time to do alignments and is not retrieving alignments

Issue - State: open - Opened by LuisGFdez over 2 years ago - 30 comments

#46 - lastz_32 fail to work

Issue - State: open - Opened by xzk-fd over 2 years ago - 8 comments

#45 - lastz parameter --queryhsplimit=keep,nowarn:200

Issue - State: open - Opened by rsharris over 2 years ago - 19 comments

#44 - map to many allele in reference genome

Issue - State: open - Opened by AlisaGU almost 3 years ago - 7 comments

#43 - whether to mask query and target?

Issue - State: open - Opened by AlisaGU about 3 years ago - 1 comment

#42 - minor fix to sequence.* suggestion

Issue - State: closed - Opened by vpbrendel about 3 years ago - 3 comments

#41 - Latest releases are missing tags

Issue - State: open - Opened by AlexWeitzel over 3 years ago - 2 comments

#40 - Build Fail (v1.04.12)

Issue - State: closed - Opened by rmandla over 3 years ago - 2 comments

#39 - Why it sometimes took LASTZ a long time to do alignments

Issue - State: open - Opened by YZ-SJTU over 3 years ago - 14 comments

#38 - Add support for output in PAF (Pairwise mApping Format)

Pull Request - State: closed - Opened by urbanslug over 3 years ago - 29 comments

#37 - truncating alignment

Issue - State: open - Opened by xiuru over 3 years ago - 1 comment

#36 - lastz_D Segmentation fault (core dumped)

Issue - State: open - Opened by AlisaGU almost 4 years ago - 18 comments

#35 - bacteria contig

Issue - State: open - Opened by AlisaGU almost 4 years ago - 7 comments

#34 - Establishing mismatch thresholds

Issue - State: open - Opened by annabananakobana almost 4 years ago - 3 comments

#33 - Error installing lastz

Issue - State: open - Opened by AllisonStander almost 4 years ago - 5 comments

#32 - Compiler error in sequences.c

Issue - State: open - Opened by weiwFu about 4 years ago - 1 comment

#31 - How can I use lastz as a PALS replacement for PILER?

Issue - State: open - Opened by rsharris about 4 years ago - 2 comments

#30 - python2 specific?

Issue - State: open - Opened by mathog about 4 years ago - 11 comments

#29 - alignment process has frozen

Issue - State: open - Opened by eleftv over 4 years ago - 4 comments

#28 - queryhspbest option is often ignored

Issue - State: open - Opened by rsharris over 4 years ago

#27 - Reported number of queries exceeding queryhsplimit is usually an overestimate

Issue - State: open - Opened by rsharris over 4 years ago

#26 - --querydepth is meaningless if --nogapped is used

Issue - State: open - Opened by rsharris over 4 years ago

#25 - Improved seeding?

Issue - State: open - Opened by cnk113 over 4 years ago - 5 comments

#24 - Multiple Genome alignment

Issue - State: closed - Opened by LemoAlex over 4 years ago - 1 comment

#23 - comparison is always false due to limited range of data type [-Werror=type-limits]

Issue - State: open - Opened by rsharris over 4 years ago - 2 comments

#22 - cast from char to signed char

Pull Request - State: closed - Opened by noguchi-k over 4 years ago - 3 comments

#21 - Compiler error in sequences.c, "strncpy output may be truncated"

Issue - State: closed - Opened by rsharris almost 5 years ago - 2 comments

#20 - bug in printing blastn format

Issue - State: open - Opened by wrf almost 5 years ago - 4 comments

#19 - Error: Structure size would exceed 2^32

Issue - State: open - Opened by darencard almost 5 years ago - 4 comments

#18 - Makefile:94: recipe for target 'seeds.o' failed

Issue - State: closed - Opened by bgbrink almost 5 years ago - 6 comments

#17 - Failed to compile by new version gcc (-Werror=misleading-indentation)

Issue - State: closed - Opened by yanlinlin82 almost 5 years ago - 15 comments

#16 - Unattached [multiple] is mis-parsed as a query file name

Issue - State: open - Opened by rsharris about 5 years ago

#15 - Possible value truncation in interpolation, for lastz_32

Issue - State: open - Opened by rsharris over 5 years ago - 1 comment

#14 - Adaptive HSP threshold with LAV produces erroneous output

Issue - State: open - Opened by rsharris over 5 years ago - 1 comment

#13 - LAV spec doen't address stanzas appearing out of order

Issue - State: open - Opened by rsharris over 5 years ago

#12 - twoBit files apparently require [multiple] even if they only contain one sequence

Issue - State: open - Opened by rsharris over 5 years ago - 2 comments

#11 - Traceback is incorrectly limited to 2G

Issue - State: open - Opened by rsharris over 5 years ago - 1 comment

#10 - Sequence length exceeds maximum for lastz_32

Issue - State: closed - Opened by alelim-bio almost 6 years ago - 1 comment

#9 - capsule file error

Issue - State: closed - Opened by nottwy about 6 years ago - 2 comments

#8 - fix [-Werror=misleading-indentation]

Pull Request - State: closed - Opened by starskyzheng about 6 years ago - 3 comments

#7 - Sequence Length exceeds maximum

Issue - State: open - Opened by Dare-IC over 6 years ago - 2 comments

#6 - Question about maf_sort.py

Issue - State: closed - Opened by 4ureliek about 7 years ago - 2 comments

#5 - Compiling issue

Issue - State: closed - Opened by ghost over 7 years ago - 5 comments

#4 - Add a break statement to fix blastn nogapped output

Pull Request - State: closed - Opened by cmdcolin over 7 years ago - 3 comments

GitHub / lastz/lastz issues and pull requests