[med-svn] [adapterremoval] 01/01: Adapt to pirs 2.0.1

[Andreas Tille]

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tille pushed a commit to branch master
in repository adapterremoval.

commit cb5db6fb34dffed7dbee027f90fd64418ebc5c11
Author: Andreas Tille <tille at debian.org>
Date:   Tue Aug 9 13:44:23 2016 +0200

    Adapt to pirs 2.0.1
---
 debian/patches/adapt-benchmarking.patch      | 9 +++++++++
 debian/patches/reduce_benchmark_length.patch | 9 +++++++++
 2 files changed, 18 insertions(+)

diff --git a/debian/patches/adapt-benchmarking.patch b/debian/patches/adapt-benchmarking.patch
index ab7cb41..7bb5e87 100644
--- a/debian/patches/adapt-benchmarking.patch
+++ b/debian/patches/adapt-benchmarking.patch
@@ -151,6 +151,15 @@
      fi
  
  
+@@ -286,7 +306,7 @@ function simulate_reads()
+                 mkdir -p "${DST}/"
+ 
+                 # -c 0 = uncompressed output
+-                if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" -i "${REFSEQ}" -c 0 -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
++                if ! ${EXEC_PIRS} simulate ${PROFILE_CLI} -x "${SIMULATED_NREADS}" -l "${readlen}" "${REFSEQ}" -c text -m "${INSERT_MEAN}" -v "${INSERT_SD}" -Q 33 -o "${DST}/reads" \
+                     > "${DST}/reads.stdout" 2> "${DST}/reads.stderr";
+                 then
+                     echo "Error simulated reads ..." > /dev/stderr
 @@ -813,7 +833,7 @@ function benchmark_se()
                  SIMULATED_MATE1="${SIMULATED_PREFIX}_${run_n}_${readlen}_1.fq"
                  SIMULATED_MATE2="${SIMULATED_PREFIX}_${run_n}_${readlen}_2.fq"
diff --git a/debian/patches/reduce_benchmark_length.patch b/debian/patches/reduce_benchmark_length.patch
index 2b99101..0098336 100644
--- a/debian/patches/reduce_benchmark_length.patch
+++ b/debian/patches/reduce_benchmark_length.patch
@@ -1,5 +1,14 @@
 --- a/benchmark/benchmark.sh
 +++ b/benchmark/benchmark.sh
+@@ -34,7 +34,7 @@ NUM_REPLICATES=10
+ # Read lengths to examine
+ # Lengths > 100 use an interpolated profile, and should therefore not be used
+ # to estimate anything other than runtime (see 'simulate_reads').
+-READ_LENGTHS=(100 200)
++READ_LENGTHS=(100)
+ 
+ # Insert sizes of reads to simulate for adapter ID
+ ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350))
 @@ -44,7 +44,7 @@ ADAPTER_ID_INSERT_SIZES=($(seq 250 5 350
  MAX_THREADS=4
  

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