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Commits on Sep 2, 2021

• Merge pull request ekg#79 from AndreaGuarracino/ingenuish

  Show description for 63fb48b
  ekg

  authored
  63fb48b

Commits on Jul 28, 2021

• handerize transclose_batch param

  AndreaGuarracino

  committed
  a1a6906

• type noise

  AndreaGuarracino

  committed
  03ff6b0

Commits on Jul 2, 2021

• don't close through Ns

  ekg

  committed
  795d7bd

Commits on Jun 16, 2021

• query/target start has to be lower than query/target end too

  AndreaGuarracino

  committed
  b653954

• Check if the coordinates are reasonable for each PAF row

  AndreaGuarracino

  committed
  52b86ee

• use stoull to convert strings in uint64_t numbers

  AndreaGuarracino

  committed
  be3673a

Commits on Mar 27, 2021

• hack: distrust cigar mismatch characters

  Show description for 9eb0982
  ekg

  committed
  9eb0982

Commits on Feb 20, 2021

• fix offsets preparation

  AndreaGuarracino

  committed
  0237199

• fix seq_name size

  AndreaGuarracino

  committed
  c298606

• remove 'the' to follow other messages convention

  AndreaGuarracino

  committed
  3110b2e

• notify the presence of empty sequences only one time

  AndreaGuarracino

  committed
  e334a24

• save the seqname only for not empty sequences

  AndreaGuarracino

  committed
  7d265f5

• notify if input FASTA contains empty sequences

  AndreaGuarracino

  committed
  5974db2

Commits on Jan 20, 2021

• fix segmentation fault with empty PAF files (or PAF files with initial empty rows)

  AndreaGuarracino

  committed
  31cc60b

Commits on Jan 6, 2021

• fix memory leak in GFA emitter

  ekg

  committed
  c7abd01

• move to memory safe mmmulti and avoid stack overflow in main

  ekg

  committed
  6387f99

Commits on Nov 23, 2020

• write smaller GFAs

  ekg

  committed
  4160084

Commits on Sep 17, 2020

• raised a warning when PAF files have no CIGAR strings ekg#61

  AndreaGuarracino

  committed
  3150fae

Commits on Sep 11, 2020

• Merge pull request ekg#63 from ekg/force-uppercase

  Show description for b5e6c31
  ekg

  authored
  b5e6c31

• resolve ekg#55 by always upper-casing the input sequence

  Show description for d7fe845
  ekg

  committed
  d7fe845

Commits on Jul 28, 2020

• checked duplicate ids in FASTA or FASTQ efficiently

  AndreaGuarracino

  committed
  4c8e867

• raised an error when two sequences with the same name are input

  AndreaGuarracino

  committed
  5754504

Commits on Jun 22, 2020

• correct handling of 'X' cigar op

  ekg

  committed
  63b1ff5

Commits on Jun 18, 2020

• also consider 'X' as a positional match case

  ekg

  committed
  2cde811

• allow extended cigar = character

  ekg

  committed
  920abf0

Commits on Apr 29, 2020

• when indexing the node/path iitrees, close the writers to stop the writer thread

  ekg

  committed
  afbb153

Commits on Apr 28, 2020

• increase chunk size for parallel_for

  ekg

  committed
  f97df5f

• keep removing reference to threads

  ekg

  committed
  85b2685

• paryforize transclosure

  ekg

  committed
  4b6b50a

• compact in parallel

  ekg

  committed
  32022a9

• remove openmp, rewrite alignment processing

  ekg

  committed
  8fa8ed7

• move to new mmulti::iitree

  ekg

  committed
  df4ab97

• avoid potential graph corruption by doing all our todos

  ekg

  committed
  35122b7

Commits on Apr 27, 2020

• allocate queues from the heap

  ekg

  committed
  aeff1d0

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