From a0ba13fae6ac668f05298132e19f0b584f1eca14 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 4 Jun 2020 16:06:03 -0600 Subject: [PATCH] Update samblaster to 0.1.26 (#22509) * Update samblaster to 0.1.26 * Delete spaces_around_identifier.patch This patch is no longer necessary according to https://github.com/GregoryFaust/samblaster/pull/44#issuecomment-638969982 * The patch is no longer needed * Update meta.yaml * Update meta.yaml Co-authored-by: Marcel Martin --- recipes/samblaster/meta.yaml | 12 +-- .../samblaster/spaces_around_identifier.patch | 96 ------------------- 2 files changed, 4 insertions(+), 104 deletions(-) delete mode 100644 recipes/samblaster/spaces_around_identifier.patch diff --git a/recipes/samblaster/meta.yaml b/recipes/samblaster/meta.yaml index 21f6ad796d938..9f6e1a30cb400 100644 --- a/recipes/samblaster/meta.yaml +++ b/recipes/samblaster/meta.yaml @@ -5,14 +5,11 @@ build: package: name: samblaster - version: '0.1.25' + version: '0.1.26' source: - url: https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.25/samblaster-v.0.1.25.tar.gz - sha256: 144bdd38ff5c15dc5032a8c63979e49d1bf1ab7cded3248e3a26b178ddd3a3be - patches: - # fix "invalid suffix on literal; C++11 requires a space between literal and identifier [-Wreserved-user-defined-literal]" - - spaces_around_identifier.patch + url: https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.26/samblaster-v.0.1.26.tar.gz + sha256: 6b42a53d64a3ed340852028546693a24c860f236fd70e90c2b24fde9dcc4fd63 requirements: build: @@ -26,5 +23,4 @@ test: about: home: https://github.com/GregoryFaust/samblaster license: MIT - summary: A tool to mark duplicates and extract discordant and split reads from sam files. - + summary: Mark duplicates in and extract discordant and split reads from SAM files. diff --git a/recipes/samblaster/spaces_around_identifier.patch b/recipes/samblaster/spaces_around_identifier.patch deleted file mode 100644 index 58b49fbacbb3f..0000000000000 --- a/recipes/samblaster/spaces_around_identifier.patch +++ /dev/null @@ -1,96 +0,0 @@ -diff -u -ur samblaster-v.0.1.25.orig/samblaster.cpp samblaster-v.0.1.25/samblaster.cpp ---- samblaster-v.0.1.25.orig/samblaster.cpp 2020-03-17 02:01:42.000000000 +0100 -+++ samblaster-v.0.1.25/samblaster.cpp 2020-03-18 14:57:24.199719994 +0100 -@@ -1115,7 +1115,7 @@ - #ifdef DEBUG - // This debug output allows the discovery of all members of a duplicate group including the read not marked as a duplicate. - // This could otherwise not be figured out from the output sam file. -- fprintf(stderr, "%"PRIu64"\t%s\t%6d\t%s\t%"PRIu64"\t%s\n", idCount, second->fields[QNAME], second->flag, insert ? "First" : "Dup", sig, second->fields[RNAME]); -+ fprintf(stderr, "%" PRIu64 "\t%s\t%6d\t%s\t%" PRIu64 "\t%s\n", idCount, second->fields[QNAME], second->flag, insert ? "First" : "Dup", sig, second->fields[RNAME]); - #endif - - // Check if the insertion actually happened. -@@ -1429,30 +1429,30 @@ - if (!state->quiet) - { - if (state->discordantFile != NULL) -- fprintf(stderr, "samblaster: Output %10"PRIu64" discordant read pairs to %s\n", discCount/2, state->discordantFileName); -+ fprintf(stderr, "samblaster: Output %10" PRIu64 " discordant read pairs to %s\n", discCount/2, state->discordantFileName); - if (state->splitterFile != NULL) -- fprintf(stderr, "samblaster: Output %10"PRIu64" split reads to %s\n", splitCount, state->splitterFileName); -+ fprintf(stderr, "samblaster: Output %10" PRIu64 " split reads to %s\n", splitCount, state->splitterFileName); - if (state->unmappedClippedFile != NULL) -- fprintf(stderr, "samblaster: Output %10"PRIu64" unmapped/clipped reads to %s\n", unmapClipCount, state->unmappedClippedFileName); -+ fprintf(stderr, "samblaster: Output %10" PRIu64 " unmapped/clipped reads to %s\n", unmapClipCount, state->unmappedClippedFileName); - } - - // Now the stats that might indicate a problem that therefore deserve reporting even if quiet set. - if (readTooLongCount > 0) - { -- fprintf(stderr, "samblaster: Found %10"PRIu64" of %10"PRIu64" (%5.3f) total read ids longer than the --maxReadLength(%d)\n." -+ fprintf(stderr, "samblaster: Found %10" PRIu64 " of %10" PRIu64 " (%5.3f) total read ids longer than the --maxReadLength(%d)\n." - "samblaster: The longest of which is %d bases long.\n", - readTooLongCount, idCount, ((double)100)*readTooLongCount/idCount, state->maxReadLength, readTooLongMax); - fprintf(stderr, "samblaster: Consider rerunning samblaster with a larger --maxReadLength.\n"); - } - if (state->ignoreUnmated) - { -- fprintf(stderr, "samblaster: Found %10"PRIu64" of %10"PRIu64" (%5.3f%%) total read ids are marked paired yet are unmated.\n", -+ fprintf(stderr, "samblaster: Found %10" PRIu64 " of %10" PRIu64 " (%5.3f%%) total read ids are marked paired yet are unmated.\n", - unmatedCount, idCount, ((double)100)*unmatedCount/idCount); - if (unmatedCount > 0) fprintf(stderr, "samblaster: Please double check that input file is read-id (QNAME) grouped.\n"); - } - if (noPrimaryIdCount > 0) - { -- fprintf(stderr, "samblaster: Found %10"PRIu64" of %10"PRIu64" (%5.3f%%) total read ids with no primary alignment.\n", -+ fprintf(stderr, "samblaster: Found %10" PRIu64 " of %10" PRIu64 " (%5.3f%%) total read ids with no primary alignment.\n", - noPrimaryIdCount, idCount, ((double)100)*noPrimaryIdCount/idCount); - if (unmatedCount > 0) fprintf(stderr, "samblaster: Please double check that input file is read-id (QNAME) grouped.\n"); - } -@@ -1485,32 +1485,32 @@ - // These first two can't produce any dups. - if (bothUnmappedIdCount > 0) - { -- fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n", -+ fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n", - typeLength, typeLength, "Both Unmapped ", - bothUnmappedIdCount, ((double)100)*bothUnmappedIdCount/idCount, (UINT64)0, (double)0, (double)0, (double)0); - } - if (unmappedOrphanIdCount > 0) - { -- fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n", -+ fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n", - typeLength, typeLength, "Unmapped Orphan/Singleton ", - unmappedOrphanIdCount, ((double)100)*unmappedOrphanIdCount/idCount, (UINT64)0, (double)0, (double)0, (double)0); - } - // All orphanDups are, of course, from mapped orphans. - if (mappedOrphanIdCount > 0) - { -- fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n", -+ fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n", - typeLength, typeLength, orphanString, - mappedOrphanIdCount, ((double)100)*mappedOrphanIdCount/idCount, orphanDupCount, - ((double)100)*orphanDupCount/mappedOrphanIdCount, ((double)100)*orphanDupCount/dupCount, ((double)100)*orphanDupCount/idCount); - } - if (bothMappedIdCount > 0) - { -- fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n", -+ fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n", - typeLength, typeLength, "Both Mapped ", - bothMappedIdCount, ((double)100)*bothMappedIdCount/idCount, bothMappedDupCount, ((double)100)*bothMappedDupCount/bothMappedIdCount, - ((double)100)*bothMappedDupCount/dupCount, ((double)100)*bothMappedDupCount/idCount); - } -- fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n", -+ fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n", - typeLength, typeLength, "Total ", - idCount, ((double)100)*idCount/idCount, dupCount, - ((double)100)*dupCount/idCount, (double)100, ((double)100)*dupCount/idCount); -@@ -1518,7 +1518,7 @@ - } - // Output the main conclusion even if we output the table. - // It includes the fact of whether or not the dups were marked or removed, and the timing info. -- fprintf(stderr, "samblaster: %s %10"PRIu64" of %10"PRIu64" (%5.3f%%) total read ids as duplicates", -+ fprintf(stderr, "samblaster: %s %10" PRIu64 " of %10" PRIu64 " (%5.3f%%) total read ids as duplicates", - (state->removeDups ? "Removed" : "Marked "), dupCount, idCount, ((double)100)*dupCount/idCount); - if ((TIMING == 0) || state->quiet) - {