Merge pull request #8103 from mppf/revcomp-investigate

Add channel.advancePastByte, use it to improve revcomp

PR #8045 added some messy rev-comp studies that improve performance by improving the I/O pattern. What the performance comes down to is two things:
 1. Copying large chunks of the input from the channel buffer in to the array to be used
 2. Using memchr to identify the relevant chunks of the input

I experimented with a version that used regexp format strings to replace the memchr call but that had unsatisfying performance.

This PR adds channel.advancePastByte in order to enable the expression of the fast I/O pattern in revcomp easily. Now the revcomp version does the following:
 * "mark" (indicate to the I/O system not to drop the buffer as we might return)
 * identify the offset of the newline (end of the sequence description)
 * identify the offset of the > (start of the next sequence)
 * "revert" (go back to where we "marked")
 * read the data again in one go with readBytes

I'm seeing a 10% speedup for this version beyond revcomp-buf.chpl, and it is much simpler.

While there, I noticed that qio_channel_advance might not set up the buffer in some cases, so added code to do that.

- [x] full local testing
- [x] docs for advancePastByte
- [x] update catch statement to specify type
- [x] check for 32-bit issues ala #8116

Closes #8105.

Reviewed by @benharsh - thanks!

modules/standard/IO.chpl

@@ -931,6 +931,8 @@ private extern proc qio_channel_write_byte(threadsafe:c_int, ch:qio_channel_ptr_
 
 private extern proc qio_channel_offset_unlocked(ch:qio_channel_ptr_t):int(64);
 private extern proc qio_channel_advance(threadsafe:c_int, ch:qio_channel_ptr_t, nbytes:int(64)):syserr;
+private extern proc qio_channel_advance_past_byte(threadsafe:c_int, ch:qio_channel_ptr_t, byte:c_int):syserr;
+
 private extern proc qio_channel_mark(threadsafe:c_int, ch:qio_channel_ptr_t):syserr;
 private extern proc qio_channel_revert_unlocked(ch:qio_channel_ptr_t);
 private extern proc qio_channel_commit_unlocked(ch:qio_channel_ptr_t);
@@ -2249,6 +2251,29 @@ proc channel.advance(amount:int(64)) throws {
   }
 }
 
+pragma "no doc"
+proc channel.advancePastByte(byte:uint(8), ref error:syserr) {
+  on this.home {
+    try! this.lock();
+    error = qio_channel_advance_past_byte(false, _channel_internal, byte:c_int);
+    this.unlock();
+  }
+}
+
+/*
+   Reads until ``byte`` is found and then leave the channel offset
+   just after it. If that byte is never found, raises an EOFError.
+ */
+proc channel.advancePastByte(byte:uint(8)) throws {
+  on this.home {
+    try! this.lock();
+    var err = qio_channel_advance_past_byte(false, _channel_internal, byte:c_int);
+    if err then try this._ch_ioerror(err, "in advanceToByte");
+    this.unlock();
+  }
+}
+
+
 // These begin with an _ to indicated that
 // you should have a lock before you use these... there is probably
 // a better name for them...

runtime/include/qio/qio.h

@@ -1266,6 +1266,9 @@ qioerr qio_channel_end_peek_cached(const int threadsafe, qio_channel_t* ch, void
 
   return err;
 }
+
+qioerr qio_channel_advance_past_byte(const int threadsafe, qio_channel_t* ch, int byte);
+
 qioerr qio_channel_begin_peek_buffer(const int threadsafe, qio_channel_t* ch, int64_t require, int writing, qbuffer_t** buf_out, qbuffer_iter_t* start_out, qbuffer_iter_t* end_out);
 
 qioerr qio_channel_end_peek_buffer(const int threadsafe, qio_channel_t* ch, int64_t advance);

runtime/src/qio/qio.c

@@ -3441,6 +3441,51 @@ qioerr qio_channel_end_peek_buffer(const int threadsafe, qio_channel_t* ch, int6
   return err;
 }
 
+qioerr qio_channel_advance_past_byte(const int threadsafe, qio_channel_t* ch, int byte)
+{
+  qioerr err=0;
+
+  if( threadsafe ) {
+    err = qio_lock(&ch->lock);
+    if( err ) {
+      return err;
+    }
+  }
+
+  // Is there room in our fast path buffer?
+  while (err==0) {
+    if( qio_space_in_ptr_diff(1, ch->cached_end, ch->cached_cur) ) {
+      size_t len = qio_ptr_diff(ch->cached_end, ch->cached_cur);
+      void* found = memchr(ch->cached_cur, byte, len);
+      if (found != NULL) {
+        ssize_t off = qio_ptr_diff(found, ch->cached_cur);
+        off += 1;
+        ch->cached_cur = qio_ptr_add(ch->cached_cur, off);
+        break;
+      } else {
+        // We checked the data in the buffer, advance to the next section.
+        ch->cached_cur = ch->cached_end;
+      }
+    } else {
+      // There's not enough data in the buffer, apparently. Try it the slow way.
+      ssize_t amt_read;
+      uint8_t tmp;
+      err = _qio_slow_read(ch, &tmp, 1, &amt_read);
+      if( err == 0 ) {
+        if (tmp == byte) break;
+        if (amt_read != 1) err = QIO_ESHORT;
+      }
+    }
+  }
+
+  if( threadsafe ) {
+    qio_unlock(&ch->lock);
+  }
+
+  return err;
+}
+
+
 qioerr qio_channel_mark_maybe_flush_bits(const int threadsafe, qio_channel_t* ch, int flushbits)
 {
   qioerr err;
@@ -3599,6 +3644,10 @@ qioerr qio_channel_advance_unlocked(qio_channel_t* ch, int64_t nbytes)
     if( use_buffered ) {
       err = _qio_buffered_behind(ch, false);
     }
+  } else {
+    if( use_buffered ) {
+      _qio_buffered_setup_cached(ch);
+    }
   }
   return err;
 }

test/studies/shootout/reverse-complement/bharshbarg/revcomp-mark-skip-read-begin.chpl

@@ -0,0 +1,88 @@
+/* The Computer Language Benchmarks Game
+   http://benchmarksgame.alioth.debian.org/
+   contributed by Ben Harshbarger
+   derived from the Rust #2 version by Matt Brubeck
+*/
+
+const table = initTable("ATCGGCTAUAMKRYWWSSYRKMVBHDDHBVNN\n\n");
+
+config const readSize = 16 * 1024;
+
+proc main(args: [] string) {
+  const stdin = openfd(0);
+  var input = stdin.reader(iokind.native, locking=false);
+  var len = stdin.length();
+  var data : [0..#len] uint(8);
+
+  sync { // wait for all process() tasks to complete before continuing
+
+    while true {
+      const descOffset = input._offset();
+      var nextDescOffset = descOffset;
+      var seqOffset = descOffset;
+      var eof = false;
+
+      // Mark where we start scanning (keep bytes in I/O buffer in input)
+      input._mark();
+
+      // Scan forward until we get to the \n (end of description)
+      input.advancePastByte(ascii("\n"));
+      seqOffset = input._offset();
+
+      try {
+        // Scan forward until we get to the > (end of sequence)
+        input.advancePastByte(ascii(">"));
+        nextDescOffset = input._offset();
+      } catch e:EOFError {
+        eof = true;
+        nextDescOffset = len;
+      }
+
+      // Go back to the point we marked
+      input._revert();
+
+      // Read until nextDescOffset into the data array.
+      input.readBytes(c_ptrTo(data[descOffset]),
+          (nextDescOffset-descOffset):ssize_t);
+
+
+      if !eof {
+        // '-3' to skip over '\n>'
+        begin process(data, seqOffset, nextDescOffset-3);
+      } else {
+        // '-2' to skip over '\n'
+        begin process(data, seqOffset, len-2);
+        break;
+      }
+    }
+  }
+
+  const stdoutBin = openfd(1).writer(iokind.native, locking=false, 
+                                     hints=QIO_CH_ALWAYS_UNBUFFERED);
+  stdoutBin.write(data);
+}
+
+proc process(data, in start, in end) {
+
+  proc advance(ref cursor, dir) {
+    do { cursor += dir; } while data[cursor] == ascii("\n");
+  }
+  while start <= end {
+    ref d1 = data[start], d2 = data[end];
+    (d1, d2) = (table[d2], table[d1]);
+    advance(start, 1);
+    advance(end, -1);
+  }
+}
+
+proc initTable(pairs) {
+  var table: [1..128] uint(8);
+
+  for i in 1..pairs.length by 2 {
+    table[ascii(pairs[i])] = ascii(pairs[i+1]);
+    if pairs[i] != "\n" then
+      table[ascii(pairs[i].toLower())] = ascii(pairs[i+1]);
+  }
+
+  return table;
+}

test/studies/shootout/reverse-complement/bharshbarg/revcomp-mark-skip-read-begin.good

@@ -0,0 +1,171 @@
+>ONE Homo sapiens alu
+CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAC
+CTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA
+GGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT
+GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA
+AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTC
+TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGG
+GTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC
+ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG
+GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA
+CAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT
+GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTC
+TCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT
+TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCT
+GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA
+CCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGC
+GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC
+TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA
+GTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT
+CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT
+TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTC
+ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG
+GGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGT
+TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG
+CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAG
+TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCG
+CCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC
+GCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG
+CCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC
+TGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCG
+CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCA
+AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC
+CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTC
+GAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC
+GTGAGCCACCGCGCCCGGCC
+>TWO IUB ambiguity codes
+TAGGDHACHATCRGTRGVTGAGWTATGYTGCTGTCABACDWVTRTAAGAVVAGATTTNDA
+GASMTCTGCATBYTTCAAKTTACMTATTACTTCATARGGYACMRTGTTTTYTATACVAAT
+TTCTAKGDACKADACTATATNTANTCGTTCACGBCGYSCBHTANGGTGATCGTAAAGTAA
+CTATBAAAAGATSTGWATBCSGAKHTTABBAACGTSYCATGCAAVATKTSKTASCGGAAT
+WVATTTNTCCTTCTTCTTDDAGTGGTTGGATACVGTTAYMTMTBTACTTTHAGCTAGBAA
+AAGAGKAAGTTRATWATCAGATTMDDTTTAAAVAAATATTKTCYTAAATTVCNKTTRACG
+ADTATATTTATGATSADSCAATAWAGCGRTAGTGTAAGTGACVGRADYGTGCTACHVSDT
+CTVCARCSYTTAATATARAAAATTTAATTTACDAATTGBACAGTAYAABATBTGCAGBVG
+TGATGGDCAAAATBNMSTTABKATTGGSTCCTAGBTTACTTGTTTAGTTTATHCGATSTA
+AAGTCGAKAAASTGTTTTAWAKCAGATATACTTTTMTTTTGBATAGAGGAGCMATGATRA
+AAGGNCAYDCCDDGAAAGTHGBTAATCKYTBTACBGTBCTTTTTGDTAASSWTAAWAARA
+TTGGCTAAGWGRADTYACATAGCTCBTAGATAWAGCAATNGTATMATGTTKMMAGTAWTC
+CCNTSGAAWATWCAAAAMACTGAADNTYGATNAATCCGAYWNCTAACGTTAGAGDTTTTC
+ATCTGGKRTAVGAABVCTGWGBTCTDVGKATTBTCTAAGGVADAAAVWTCTAGGGGAGGG
+TTAGAACAATTAAHTAATNAAATGCATKATCTAAYRTDTCAGSAYTTYHGATRTTWAVTA
+BGNTCDACAGBCCRCAGWCRTCABTGMMAWGMCTCAACCGATRTGBCAVAATCGTDWDAA
+CAYAWAATWCTGGTAHCCCTAAGATAACSCTTAGTGSAACAWTBGTCDTTDGACWDBAAC
+HTTTNGSKTYYAAYGGATNTGATTTAARTTAMBAATCTAAGTBTCATYTAACTTADTGTT
+TCGATACGAAHGGCYATATACCWDTKYATDCSHTDTCAAAATGTGBACTGSCCVGATGTA
+TCMMAGCCTTDAAABAATGAAGAGTAACTHATMGVTTAATAACCCGGTTVSANTGCAATT
+GTGAGATTTAMGTTTAMAAYGCTGACAYAAAAAGGCACAMYTAAGVGGCTGGAABVTACG
+GATTSTYGTBVAKTATWACCGTGTKAGTDTGTATGTTTAAAGGAAAAAGTAACATARAAA
+GGTYCAMNYAAABTATAGNTSATANAGTCATCCTATWADKAACTRGTMSACDGTATSAYT
+AAHSHGTAABYGACTYTATADTGSTATAGAGAAATCGNTAAAGGAAATCAGTTGTNCYMV
+TNACDRTATBNATATASTAGAAMSCGGGANRCKKMCAAACATTNAGTCTRMAATBMTACC
+CGTACTTCTBGDSYAATWGAAAATGACADDCHAKAAAYATATTKTTTTCACANACWAGAA
+AKATCCTTATTAYKHKCTAAACARTATTTTDATBTVWCYGCAATACTAGGKAAASTTDGA
+MGGCHTTHAATVCAHDRYAGGRCTATACGTCMAGAGAGCTBTHGNACARTCCBDCTAAGA
+GCGGCTTTARTAAAGAATCCNAGTAWBTGACTTGAATTACWTVACAGAAABCAATNAAAC
+CGTNTRANTTGAYCMAWBADTANABRGGTKTHTWTAGTTVCTMBKTAGMTVKCCAGCANT
+TVAGSWTTAGCCGCRHTTTCCTTHNTATTAAGAAGAATAGGMTRAARTCTABGTACDTTT
+TATAAVDHAHTATAGATCCTAGTAAGYTWATDWCATGAGGGATAGTAAMDMNGBASTWAM
+TSTATRBAYDABATGTATATYCGCACTGTTTTAACMCWBTATAWAGTATBTSTATVTTAR
+CCTMTTAAKADATCAACTAATYTSVTAKGDATTATGCKTCAYCAKAATACTTKAANGAGT
+ATTSDAGATCGGAAATACTTAAYAAVGTATMCGCTTGTGTDCTAATYTATTTTATTTWAA
+CAGWRCTATGTAGMTGTTTGTTYKTNGTTKTCAGAACNTRACCTACKTGSRATGTGGGGG
+CTGTCATTAAGTAAATNGSTTABCCCCTCGCAGCTCWHTCGCGAAGCAVATGCKACGHCA
+ACAKTTAATAACASAAADATTWNYTGTAATTGTTCGTMHACHTWATGTGCWTTTTGAAHY
+ACTTTGTAYAMSAAACTTAADAAATATAGTABMATATYAATGSGGTAGTTTGTGTBYGGT
+TWSGSVGWMATTDMTCCWWCABTCSVACAGBAATGTTKATBGTCAATAATCTTCTTAAAC
+ARVAATHAGYBWCTRWCABGTWWAATCTAAGTCASTAAAKTAAGVKBAATTBGABACGTA
+AGGTTAAATAAAAACTRMDTWBCTTTTTAATAAAAGATMGCCTACKAKNTBAGYRASTGT
+ASSTCGTHCGAAKTTATTATATTYTTTGTAGAACATGTCAAAACTWTWTHGKTCCYAATA
+AAGTGGAYTMCYTAARCSTAAATWAKTGAATTTRAGTCTSSATACGACWAKAASATDAAA
+TGYYACTSAACAAHAKTSHYARGASTATTATTHAGGYGGASTTTBGAKGATSANAACACD
+TRGSTTRAAAAAAAACAAGARTCVTAGTAAGATAWATGVHAAKATWGAAAAGTYAHVTAC
+TCTGRTGTCAWGATRVAAKTCGCAAVCGASWGGTTRTCSAMCCTAACASGWKKAWDAATG
+ACRCBACTATGTGTCTTCAAAHGSCTATATTTCGTVWAGAAGTAYCKGARAKSGKAGTAN
+TTTCYACATWATGTCTAAAADMDTWCAATSTKDACAMAADADBSAAATAGGCTHAHAGTA
+CGACVGAATTATAAAGAHCCVAYHGHTTTACATSTTTATGNCCMTAGCATATGATAVAAG
+>THREE Homo sapiens frequency
+ATATTTATCTTTTCACTTCCTACATTGGTCAGACCATTATTCGACACGTGGCGTCATTTT
+GTCATACCGGGTAATGTTGGAAACAAAACGTACTGATAAAATACTGAGTTGTAAACTCTA
+ATCAGATAACGCGCTTGGATATTAAGATTCACACAGGGGTTTCGGCTGTAAAAAAACTTG
+TGGAGCTGTTCTGGGACAGATAAGTTGTACCTCGTACTTAGCTAATTAATGAACCAACTG
+ATTACGATAGAACAATTCTGAGGCCGCCAGGACAGCCAAATTTTAATCTTATAAAGCTGG
+AAACAGCCGGTATTAGCTTCTCGCATACTTTGCCTGCATTGGTACCTTACAGATATCAGC
+GTAGTCATATACACCTCGGTCTCAGCTAAGCTTGTATCTCTTAGAGTAGTTCAAAGATAG
+TGGACAATACCTGTGGAATCGATTGCAGATATGGATTTATTTAACTACTGAGTCTCATTC
+ACAAGCTAAGCAAGGAGCACGTTTTGGTGCCGGCATACCGATTTGCTATCATGTCAGCAA
+ATTTGCGTTGTATTCCTAGTTGCACCCATTAAGGCCACACTCCGAACCTAATTATTACAT
+CGCAAAGACATGTACGAAGGACCCGATGTCGAATAGAAGGGAGGACTGTTCATTGGAAGC
+TAGACCAGAGGAATCGCAAAGATGCAACTCTTACAATAAAAATCTAATTTCAGTCAACAC
+GCAATTTCTATAAGGTTTCCGATAATAATGAACCGTCTTCCACAGGGGAATTTGCCATGC
+TCGTAAAAGTAGTTAATCCAAGTAGAAGAAATTTTGATAATGTTTTAAGTTGGCACGAAG
+GAATTCAGAGAGATCTTACCTAACAAAGGCATTAGTAGATGTTCCTTGGTTCACACTCGG
+TCAATCAGAGCACATACTACGGGCGATACCGGGAATGACACAACATCAATGAGATTGTTA
+AGTGAGGTAATTGACTTTAGAGGACTCGATCAGTATACTGTCACTATGAACATCGTATTA
+ATTGTTATCCGATATATACACCACCGATTTGCTTGTGCAAGGTTACAGACCCATTCGATA
+AATACAAACACGGAGCGATATTATTTAAGGAGTGCTGTCTTCAAAAGAATTATTCCCACA
+CCGACATAAGAACTTCGCTCCGTCATTCCAGATTTAAATAACATAACGTAACGCTTTGCT
+GATAACATAACATAACCGAGAATTTGCTTAGGAAATTTGGAGCAATATTGCATTGTTTCT
+CAGTCATCACAAGGCCCGCCAAAGAACTCTGAGAATCAGGATTCAACATGATTGGTAAGA
+CTCTATATATATAACTTAATTCTTGTGTCCGGAGATAGAAAGAGGACGAGAGATACTACG
+AAAGAAAGTGTACTTCGATGTATCAATTCAGACGCCTTCTCTATCATCAACATTATAGGT
+CTCGTATATGCTCGGCGCGATCTGCTTCTCTCCGCCAATAGCCCCATAGTGTATTTCAAG
+CGCAGTAACAGTGAAATCGTTACGAAGGTAGGGATGTTGCTTATAATTGTCGTAACTTAT
+CGCTTATGTATCTTTCAAGAATGAACGGCAGCATATACATACGTTCTACCTTTAGCTACA
+AAGCATCCATATACTCCCTCTCATGATTGAAACTCTTCCCTATTTTGTAGCCAATAGTGA
+AAGCGTATTAGTATAAATTCGTCGGTTTTTCACTCGCAACTGTTATACTCTGCAAACAAA
+CGAAAGCCTCATAGTACAAACCTAAAGCTACATACTTCATCATTGGCAGACCAGTGGCGG
+TATTTCTACGGAAGCATCACTATAGATATAAAGTTTCCCTTCATGTACGTCTGTTAACCA
+TATCACAAGAAACTGCTATCTCTGTCACGTAACAATTCACGCGCCTTATCGCCAAATGTT
+CATATATGCGCGGTATACGTATGAACGAATACTAATTAGTATAACGGAGGATTCACGGGA
+GGGATACTTGGGGCATTTATAAATCGTCTAAAAATTTTCTATCAGCACTTGCGGGTTATA
+GTGGATTACTAGGCAACATAATATTCTGTATTGGTCCAAATGACGCTATAGATAAATTAG
+CAAAATACATTGTTTCCATTTATGTAAGTCGAAACTCCAGGACTCCCGGGAACCAGTTAA
+ACCGTCTGGAAAAGACACATTGTGAGCGGGACTTCAATGATAGCTTTCAATGAGCTTCTC
+ATGCTTGGGGTCTGTACATATATGTTGGCGAAATTATCGTCTGTATTCTGTTATGCTTTG
+ATCATGGGTTATTAGTATAGTGTCCGGTTAAGTACCAATACCGCTAGAGACCCGACCTAA
+GTCGATAACTAACGATCATCGACGTAAGGATCGTCTCGATCAGTACTTCAGTCTAGATCT
+GGGAATAGTAACTCGTTAGTGAACTATGTCGTGTCATAACTCTAAAATGCAATCAAATCT
+TATTATTGAGTATTGATTATATAAAGCATCCGCTTAGCTTTACCCTCAAATGTTATATGC
+AATTTAAAGCGCTTGATATCGTCTACTCAAGTTCAGGTTTCACATGGCCGCAACGTGACG
+TTATTAGAGGTGGGTCATCATCTCTGAGGCTAGTGATGTTGAATACTCATTGAATGGGAA
+GTGGAATACCATGCTCGTAGGTAACAGCATGACCTATAAAATATACTATGGGTGTGTGGT
+AGATCAATATTGTTCAAGCATATCGTAACAATAACGGCTGAAATGTTACTGACATGAAAG
+AGGGAGTCCAAACCATTCTAACAGCTGATCAAGTCGTCTAAAAACGCCTGGTTCAGCCTT
+AAGAGTTATAAGCCAGACAAATTGTATCAATAGAGAATCCGTAAATTCCTCGGCCAACCT
+CTTGCAAAGACATCACTATCAATATACTACCGTGATCTTAATTAGTGAACTTATATAAAT
+ATCTACAACCAGATTCAACGGAAAAGCTTTAGTGGATTAGAAATTGCCAAGAATCACATT
+CATGTGGGTTCGAATGCTTTAGTAATACCATTTCGCCGAGTAGTCACTTCGCTGAACTGT
+CGTAAATTGCTATGACATAATCGAAAAGGATTGTCAAGAGTCGATTACTGCGGACTAATA
+ATCCCCACGGGGGTGGTCTCATGTCTCCCCAGGCGAGTGGGGACGGTTGATAAACACGCT
+GCATCGCGGACTGATGTTCCCAGTATTACATAGTCACATTGGATTGCGAGTAGTCTACCT
+ATTTATGAGCGAGAGATGCCTCTAACTACTTCGACTTTTAAAACCTTTCCACGCCAGTAT
+TCGGCGAAAGGGAAGTATTAAGGGTTGTCATAATTAAGCTGATACCACTTCAGACTTTGC
+TCTACTTCTGTCTTTCATTGGTTTAGTAAAGTCTGTCCATTCGTCGAGACCGTCTTTTGC
+AGCCTCATTCTACCAACTGCTCCGACTCTTAGTCTGCTTCTCCCAGCGTTATAACAAGAG
+GCATTTTGTCATCCTTAAAACAATAATAAAGAACTCGGAGCACTGATATAATGACTGAAT
+TAGAACCGCTTAAAAATACAACGAATAGATAAGACTATCGGATAAGATCTAATATGTAGT
+GATTAAGCCCTTTATTAATTAATAATAGTTACCCTTTCTGATGTAACGCGACATATTACG
+ATTTAGTGGCACGTCTGAATTGCAAAGCAGATCTCTACCCGATTTTTATTATAAATCCCG
+TATACATCTTGACTTGAGTAATTGTTCATCTTTTTATATCTCTTCGTACTACAAATAATT
+AATATCTCAACCCGTATTGTGTGATTCTAATTACCAACAGAATACGAGGAGGTTTTTGCT
+TAGGGCCATATATAATGAATCTATCTCGTTTATTCGCGGAACCCGAGATAACATTACGAT
+GTAACTATTTTAGAGAACTTAATACAAGAAACATTGCTGATTACTCATAACTAAATGCTT
+GGTAATATATCCTCAGTGCCCCTACCATCTTTTACGCAGGGATGTAATTACTTAGGATTC
+ATTGTGTAAGAATTACAATGAACGATGGATATGAAGGCATGTTGCGAGGTGTTCCTTGGT
+ATGTGAAGTTCGCAGGGCAACAAAAATTTCGCAGAATAGGCCTCAAAGTATTGGTAAAGA
+AGACAACTAATCATCACGAGCTTCTGATATCAATACGAACGAGTCCTGTGATGGATGAAA
+GAAAGTCGTATCGAAAATGTCAAGAGTCTGCCCAATGTAACTTACTTCAAAAAATAACGC
+TTCCGCCAAGTACGTTCGAATAAACGTAATTTTAAAAATACATAAGGGGTGTTAGAAAGT
+AAGCGACGGGATATAAGTTAGACTCAAGATTCCGCCGTAAAACGAGACTGATTCCGAAGA
+TTGTTCGTGGATCTGGTCATGACTTTCACTGAGTAAGGAGTTTCGACATATGTCAATAAA
+CACAAAAATAGAAGCTATTCGATCTGAAAAATATTAGGACAAGAAACTATCTCACGCTAG
+CCCAGAATATTCACTCACCCACGGGCGATACTAAAGCACTATATAGTCGCGTGATTACTA
+TACATATGGTACACATAAGAATCACGATCAGGTTCTCAATTTTCAACAATATATGTTTAT
+TTGCATAGGTAATATTAGGCCTTTAAGAGAAGGATGGGTGAGATACTCCGGGGATGGCGG
+CAATAAAGAAAAACACGATATGAGTAATAGGATCCTAATATCTTGGCGAGAGACTTAAGG
+TACGAATTTTGCGCAATCTATTTTTTACTTGGCCAGAATTCATGTATGGTATAAGTACGA
+ACTTTTTTGATCACTTTCATGGCTACCTGATTAGGATAGTTTGAGGAATTTCCCAAATAT
+ACCGATTTAATATACACTAGGGCTTGTCACTTTGAGTCAGAAAAAGAATATAATTACTTA
+GGGTAATGCTGCATACATATTCTTATATTGCAAAGGTTCTCTGGGTAATCTTGAGCCTTC
+ACGATACCTGGTGAAGTGTT

test/studies/shootout/reverse-complement/bharshbarg/revcomp-mark-skip-read-begin.perfkeys

@@ -0,0 +1,2 @@
+real
+verify:4166671:CCGACTATTGTAGTTATGGG

test/studies/shootout/reverse-complement/bharshbarg/revcomp-mark-skip-read-begin.suppressif

@@ -0,0 +1,2 @@
+CHPL_LAUNCHER <= slurm
+CHPL_LAUNCHER <= aprun

test/studies/shootout/reverse-complement/revcomp.graph

@@ -1,6 +1,6 @@
-perfkeys: real, real, real, real, real
-files: revcomp.dat, revcomp-begin.dat, revcomp-blc.dat, revcomp-buf.dat, revcomp-line.dat
-graphkeys: release version, revcomp-begin, Brad version, Buffered, BufferedLine
+perfkeys: real, real, real, real, real, real
+files: revcomp.dat, revcomp-begin.dat, revcomp-blc.dat, revcomp-buf.dat, revcomp-line.dat, revcomp-mark-skip-read-begin
+graphkeys: release version, revcomp-begin, Brad version, Buffered, BufferedLine, mark-skip-read
 graphtitle: Reverse-complement Shootout Benchmark
 ylabel: Time (seconds)
 graphname: revcomp