Far too large pull - grid/slurm support, checkpointing, extra features#73

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flowers9 wants to merge 57 commits intoxiaochuanle:masterfrom flowers9:master

+4,745-4,501

Commits on Feb 19, 2019

This branch supports grid/slurm (and possibly other remote queueing
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Commits on Mar 22, 2019

Mild reformat and warning removal
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removed id from seq index
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Commits on Mar 25, 2019

remove rand() calls, reformatting
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changed min/max read id to overlap counts
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minor cleanup
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Commits on Mar 26, 2019

cleaned up packdb
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Commits on Apr 1, 2019

added read/candidate ordering for improved throughput
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refactored candidate thread loop
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made fasta to pac conversion restartable
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Commits on Apr 3, 2019

testing reordering reads
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Commits on Apr 4, 2019

added branch for number of reads vs u4_t
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Commits on Apr 9, 2019

added options for reordering and preprocessing
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Commits on Apr 10, 2019

more prep towards reordering properly
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added option for binary output to mecat2pw
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Commits on Apr 12, 2019

shifting candidate handling to new format
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Commits on Apr 13, 2019

Merge branch 'master' of https://github.com/xiaochuanle/MECAT
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Commits on Apr 16, 2019

added MECAT2 defaults, fixed memory reduction bugs
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Commits on Apr 17, 2019

random cleanup: stderr -> cerr, timer cleanup
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trashed reorder attempt
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changed sorting ec_list to better order reads
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cleaned up some comparison functions
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added k/m/g suffixes to integer options
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Commits on Apr 18, 2019

changed some fprintf to use cerr instead
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convert id_list to vector<>
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changed cns_table to vector
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whoops, forgot to check for errors before commiting
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changed CnsAln and CnsAlns to vectors
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Commits on Apr 19, 2019

removed some duplicate and obsolete code
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converted M5Record to use vector instead of malloc
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changed DiffRunningData from malloc to vectors
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Commits on Apr 22, 2019

added max_aln_size back in after accidentally removing it
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Commits on Apr 23, 2019

finished changes from defined (large) array buffers to vectors and strings
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Commits on Apr 29, 2019

remove extra buffer read/write when getting alignments
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Commits on May 1, 2019

moved to copy() over memcpy, unified left/right buffers
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in the middle of testing, this is a save point
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Commits on May 3, 2019

still working on bug, but got rid of bsearch in dw.cpp
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fixed bugs, improved speed of alignment finding
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increase RM from 100k to 500k
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Commits on May 4, 2019

back to static allocation
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perform better static sizing of GetAlignment() buffers
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Commits on May 5, 2019

added exit files to allow detection of failed execution of sub-tasks
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Commits on May 7, 2019

general cleanup, moved error_rate to options
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cleaned up Align() a bit
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Commits on May 9, 2019

minor pre-alloc fix
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char -> uint1, pthread mutex -> c++11
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minor cleanup and reformatting
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Commits on May 15, 2019

narrowed d_path buffer to reflect cutoff
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comments, refined d_path size
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Commits on May 21, 2019

include cleanup, corrected Align() loop termination
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more cleanup of header file includes
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Commits on May 24, 2019

added timing to output
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Commits on Jun 14, 2019

Minor cleanup, added lto, moved if out of inner Align loop
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type cleanup, header file cleanup
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Commits on Jun 19, 2019

vectorization of mecat2cns inner loop, some cleanup
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Commits on Jun 21, 2019

improved inner loop
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Commits on Jun 24, 2019

random cleanup
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